tag:blogger.com,1999:blog-315110292589233062024-03-16T12:12:51.663+11:00Edwards Lab<b>The unofficial blog and webpage of the genomics, molecular evolution and bioinformatics lab of Dr Richard Edwards, University of West Australia (Perth, Australia).</b>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.comBlogger190125tag:blogger.com,1999:blog-31511029258923306.post-44056307911818853482024-01-04T11:12:00.004+11:002024-01-04T11:12:15.993+11:00Happy New Year! Updates coming soon...It's been a really busy year or so, getting the Minderoo OceanOmics Centre at UWA fully staffed operational, and blog content has suffered as a result. Stay tuned for a backlog of publications and other news - including some of the first outputs to come out of <a href="https://www.ncbi.nlm.nih.gov/bioproject/1046164" target="_blank">Ocean Genomes</a>, and exciting updates to the <a href="https://www.uwa.edu.au/oceans-institute">Oceans Insitute</a> strategy.Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-60931505188966563652023-07-19T14:28:00.002+10:002023-07-29T22:52:37.433+10:00The OceanOmics Centre is hiring! Research technician positions available<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiY3utmg4JipGOCpIJQ7LFSh_b51fOyt5dHuiwWu-NFoAl_oNmc34okigyaWAEMVrAamoZOcyjM87QHnSXBT4Rp_jzKEr0wFv_Vi0Pf3RWx-RsT2g5SCGedJvbfD0KfYPwwlst4nmfaK52SBdfrDiwlgVN_YNezPY7y2wbFVUL1PVcuM43oOFTsNedZ/s1024/OGL%20-%20Corridor%20view%20%28fish%29.jpeg" style="padding: 0 1em; text-align: center; clear: right; float: right;"><img alt="" border="0" width="220" data-original-height="768" data-original-width="1024" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiY3utmg4JipGOCpIJQ7LFSh_b51fOyt5dHuiwWu-NFoAl_oNmc34okigyaWAEMVrAamoZOcyjM87QHnSXBT4Rp_jzKEr0wFv_Vi0Pf3RWx-RsT2g5SCGedJvbfD0KfYPwwlst4nmfaK52SBdfrDiwlgVN_YNezPY7y2wbFVUL1PVcuM43oOFTsNedZ/s400/OGL%20-%20Corridor%20view%20%28fish%29.jpeg"/></a>We are recruiting two new positions for the <b>Minderoo OceanOmics Centre at UWA</b>: a <a href="https://external.jobs.uwa.edu.au/cw/en/job/512661" target="_blank">Marine Genomics Research Technician</a> and an <a href="https://external.jobs.uwa.edu.au/cw/en/job/514981" target="_blank">eDNA Research Technician / Scientific Officer</a>. These are both full-time two-year positions (with likely opportunities for extension), and applications close <b>11:55 PM AWST on Sunday, 6 August 2023</b>. Please see the link below to find out more. Informal enquiries are also welcome - please contact <a href="https://research-repository.uwa.edu.au/en/persons/rich-edwards">Rich Edwards</a>.</p>
<p>We are seeking two new members of the technical support team for the OceanOmics Centre, particularly with respect to all aspects of DNA sequencing (sample extraction, library preparation and setting up sequencing runs). You’ll get to play with the latest sequencing technologies, including Illumina NovaSeq/NextSeq, PacBio Sequel/Revio, and ONT PromethION P24. One role will focus on marine vertebrate reference genomes, and associated techniques (e.g. high molecular weight DNA extract, and HiC proximity ligation). The other role has an environmental DNA (eDNA) focus, with more emphasis on Illumina sequencing and liquid handling robots.</p>
<h2 id="abouttheteam">About the team</h2>
<p>The Minderoo OceanOmics Centre at UWA is a partnership between UWA and Minderoo Foundation to undertake research and development under the direction of Minderoo’s OceanOmics Program. Part of Minderoo’s Flourishing Oceans initiative, this ambitious program aims to revolutionise ocean conservation through application of novel environmental DNA technologies. This includes the development of innovative laboratory and computational approaches to optimise and scale collection, processing and analysis of environmental DNA (eDNA) from marine environments, as well as generate a comprehensive reference library of marine vertebrate genome data. All data produced as part of the OceanOmics program will be subject to rigorous QA/QC and released publicly through open access repositories.</p>
<p>Located in the Bayliss Building on the UWA Crawley Campus, the OceanOmics Centre combines a joint Ocean Genomes Laboratory, an OceanOmics/eDNA Laboratory, and Computational Biology Services. Equipped with the latest high-throughput sequencing technology, liquid handling robotics, flow cytometry, and computational infrastructure, the centre is staffed by a collaborative team of scientists (from both Minderoo and UWA) and UWA technical staff. Core centre operations support the Minderoo OceanOmics Program, under the direction of senior Minderoo employees.</p>
<p>UWA staff, including this postholder, are part of the UWA Oceans Institute, a multidisciplinary research institution with core offices in the nearby Indian Ocean Marine Research Centre building, and liaise closely with Minderoo employees for day-to-day operations.</p>
<p>For more details, and to apply, visit the UWA jobs site: <a href="https://external.jobs.uwa.edu.au/cw/en/job/512661">https://external.jobs.uwa.edu.au/cw/en/job/512661</a> and <a href="https://external.jobs.uwa.edu.au/cw/en/job/514981">https://external.jobs.uwa.edu.au/cw/en/job/514981</a>.</p>
<p>We are also recruiting students for <a href="http://edwardslab.blogspot.com/2023/06/three-pawsey-internship-projects.html">three Pawsey student internships</a>.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-64768039979005965212023-06-29T22:50:00.001+10:002023-06-29T22:58:45.266+10:00Three Pawsey Internship projects available for the Ocean Genomes Project<p>We have three <a href="https://pawsey.org.au/supercomputing/training/pawsey-internships-call-for-students-2021-2022/">Pawsey student internships</a> available this summer with the Ocean Genomes Laboratory in the Minderoo OceanOmics Centre at UWA. Closing date: <strong>07 August, 2023 at 17:00 AWST (Perth time)</strong>. This is a 10-week, paid program open to exceptional undergrad (2nd/3rd year), Honours, Master’s and PhD students. Apply at the <a href="https://jobs.csiro.au/job/Pawsey-Supercomputing-Centre-Summer-Internships/941134910/">CSIRO Application page</a>. Please get in touch if you want to know more and/or are interested in a student research project in the lab.</p>
<h2 id="optimisingworkflowsforwholegenomeassemblyformarinevertebratesproject04">Optimising workflows for whole genome assembly for marine vertebrates (Project #04)</h2>
<p>The biodiversity of marine vertebrates is critical for the health of our ocean’s ecosystem, but is under immediate threat from climate change, pollution, overfishing and habitat destruction. To advance our understanding of how best to protect and sustain our ocean life, global efforts are underway (such as the Vertebrate Genome Project; VGP) to establish a complete library of high-quality reference genomes for all ~22,000 marine vertebrates. </p>
<p>Reference genomes are pivotal not only for answering fundamental questions in marine biology and evolution, but also for guiding the conservation of species most at risk within our changing oceans, and for accurately monitoring biodiversity. </p>
<p>This project utilizes data generated in-house, either by Illumina short-read or PacBio high-fidelity long-read sequencing of Australian marine vertebrate species. The primary objective is to optimize analysis workflows on Pawsey, encompassing the entire life cycle of the data from its raw format to the ultimate outcome of a high-quality assembled genome. We have data across a diverse range of species covering small to large genome sizes.</p>
<h2 id="acontainerisedpawseyworkflowfordiploidocusproject10">A containerised Pawsey workflow for Diploidocus (Project #10)</h2>
<p>Bioinformatics in general, and genomics specifically, is replete with complex workflows that do not translate easily to HPC. Frequently, genomics pipelines will incorporate many different tools and/or in-built functions with very different computational requirements in terms of multithreading, memory requirements and IO pressures. The <a href="https://github.com/slimsuite/diploidocus">Diploidocus</a> genome curation pipeline exemplifies this problem with some lengthy single-processor steps building on data produced by highly parallelised tools, such as minimap2. As well as adapting a specific mission-critical tool, this project will help identify and establish some general principles for optimising genomics code/workflows for running on Setonix.</p>
<p>Diploidocus is a published genome curation and clean-up tool that utilises several different underlying bioinformatics tools and in-built algorithms. Different steps (and tools) in the pipeline have markedly different CPU, IO and memory requirements, including some lengthy non-parallelised portions. This makes it hard to run efficiently on HPC without wasting resource allocation and/or failing to take advantage of parallelisation when available.</p>
<p>The expected outcome of this project is a Nextflow workflow for the deployment of the Diploidocus pipeline on HPC. This will (a) increase in-house efficiency of HPC usage, and (b) make Diploidocus more attractive as a tool to other research groups.</p>
<h2 id="acontainerisedpawseyworkflowhighthroughputphylogenomicsproject14">A containerised Pawsey workflow high throughput phylogenomics (Project #14)</h2>
<p>This project aims to produce a robust and efficient phylogenomics workflow for whole genome sequencing data. </p>
<p>One important application of genome assemblies is to test and improve the taxonomic classification of species using large-scale genome-wide phylogenetics, known as phylogenomics. There is a previously developed Snakemake workflow for the rapid generation of phylogenomic trees from low- to mid-coverage whole genome shotgun sequencing data. This pipeline (1) creates multiple rapid draft assemblies; (2) identifies an optimal set of orthologous genes per species using BUSCO and <a href="https://github.com/slimsuite/buscomp">BUSCOMP</a>; (3) generates a multiple sequence alignment per gene; (4) generates a phylogenetic tree per gene; and (5) generates a consensus tree from all the individual gene trees.</p>
<p>There is now a requirement to (1) update the pipeline to be optimised for the high-coverage draft and reference genomes created by the Ocean Genomes Project, and (2) convert this pipeline from PBS/Snakemake to SLURM/Nextflow in-line with other genomics workflows being developed at the Minderoo OceanOmics Centre at UWA. </p>
<p>This project will adapt the <a href="https://github.com/slimsuite/wgs2tree">wgs2tree</a> workflow to optionally start from a set of existing genome assemblies and BUSCO orthologue annotations and implement a Nextflow/SLURM workflow optimised to run efficiently on Pawsey.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-89432107723426105052023-06-22T20:36:00.020+10:002023-06-29T23:18:41.760+10:00The Minderoo OceanOmics Centre at UWA is hiring - lab manager position available<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiY3utmg4JipGOCpIJQ7LFSh_b51fOyt5dHuiwWu-NFoAl_oNmc34okigyaWAEMVrAamoZOcyjM87QHnSXBT4Rp_jzKEr0wFv_Vi0Pf3RWx-RsT2g5SCGedJvbfD0KfYPwwlst4nmfaK52SBdfrDiwlgVN_YNezPY7y2wbFVUL1PVcuM43oOFTsNedZ/s1024/OGL%20-%20Corridor%20view%20%28fish%29.jpeg" style="padding: 0 1em; text-align: center; clear: right; float: right;"><img alt="" border="0" width="220" data-original-height="768" data-original-width="1024" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiY3utmg4JipGOCpIJQ7LFSh_b51fOyt5dHuiwWu-NFoAl_oNmc34okigyaWAEMVrAamoZOcyjM87QHnSXBT4Rp_jzKEr0wFv_Vi0Pf3RWx-RsT2g5SCGedJvbfD0KfYPwwlst4nmfaK52SBdfrDiwlgVN_YNezPY7y2wbFVUL1PVcuM43oOFTsNedZ/s400/OGL%20-%20Corridor%20view%20%28fish%29.jpeg"/></a>We are recruiting a new <a href="https://external.jobs.uwa.edu.au/cw/en/job/514000" target="_blank">lab manager position</a> for the <b>Minderoo OceanOmics Centre at UWA</b>. This is a full-time three-year position, available at Level 6 or 7, depending on experience. Applications close <b>11:55 PM AWST on Thursday, 13 July 2023</b>. Please see the link below to find out more. Informal enquiries are also welcome - please contact <a href="https://research-repository.uwa.edu.au/en/persons/rich-edwards">Rich Edwards</a>.</p>
<p>We are seeking a detail-oriented professional who possesses excellent organisational and managerial skills, ideally with a strong scientific background. Your operations experience will ensure smooth functioning of the laboratory, promoting a safe, productive and efficient working environment. As lab manager, you will work closely with the Lead Academic of the OceanOmics Centre to optimise operations to support the goals of Minderoo’s OceanOmics Program.</p>
<h2 id="abouttheteam">About the team</h2>
<p>The Minderoo OceanOmics Centre at UWA is a partnership between UWA and Minderoo Foundation to undertake research and development under the direction of Minderoo’s OceanOmics Program. Part of Minderoo’s Flourishing Oceans initiative, this ambitious program aims to revolutionise ocean conservation through application of novel environmental DNA technologies. This includes the development of innovative laboratory and computational approaches to optimise and scale collection, processing and analysis of environmental DNA (eDNA) from marine environments, as well as generate a comprehensive reference library of marine vertebrate genome data. All data produced as part of the OceanOmics program will be subject to rigorous QA/QC and released publicly through open access repositories.</p>
<p>Located in the Bayliss Building on the UWA Crawley Campus, the OceanOmics Centre combines a joint Ocean Genomes Laboratory, an OceanOmics/eDNA Laboratory, and Computational Biology Services. Equipped with the latest high-throughput sequencing technology, liquid handling robotics, flow cytometry, and computational infrastructure, the centre is staffed by a collaborative team of scientists (from both Minderoo and UWA) and UWA technical staff. Core centre operations support the Minderoo OceanOmics Program, under the direction of senior Minderoo employees. UWA staff, including this postholder, are part of the UWA Oceans Institute, a multidisciplinary research institution with core offices in the nearby Indian Ocean Marine Research Centre building, and liaise closely with Minderoo employees for day-to-day operations.</p>
<p>For more details, and to apply, visit the UWA jobs site: <a href="https://external.jobs.uwa.edu.au/cw/en/job/514000">https://external.jobs.uwa.edu.au/cw/en/job/514000</a>.</p>
<p>Watch this space for some further opportunities coming soon: two laboratory research technicians, and three Pawsey student internships.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-82830238796480734382022-11-23T17:06:00.002+11:002022-11-23T17:06:19.561+11:00Minderoo OceanOmics Centre at UWA Grand Opening<div class="separator" style="clear: both;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiY3utmg4JipGOCpIJQ7LFSh_b51fOyt5dHuiwWu-NFoAl_oNmc34okigyaWAEMVrAamoZOcyjM87QHnSXBT4Rp_jzKEr0wFv_Vi0Pf3RWx-RsT2g5SCGedJvbfD0KfYPwwlst4nmfaK52SBdfrDiwlgVN_YNezPY7y2wbFVUL1PVcuM43oOFTsNedZ/s1024/OGL%20-%20Corridor%20view%20%28fish%29.jpeg" style="display: block; padding: 1em 0; text-align: center; "><img alt="" border="0" width="568" data-original-height="768" data-original-width="1024" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiY3utmg4JipGOCpIJQ7LFSh_b51fOyt5dHuiwWu-NFoAl_oNmc34okigyaWAEMVrAamoZOcyjM87QHnSXBT4Rp_jzKEr0wFv_Vi0Pf3RWx-RsT2g5SCGedJvbfD0KfYPwwlst4nmfaK52SBdfrDiwlgVN_YNezPY7y2wbFVUL1PVcuM43oOFTsNedZ/s400/OGL%20-%20Corridor%20view%20%28fish%29.jpeg"/></a></div>
<p>The Grand Opening of the Minderoo OceanOmics Centre at UWA is only a day away! Join the launch of the Centre online from 4:40 to learn more about the inspiration and the vision behind this project, which aims to harness environmental DNA and genomics for marine conservation: <a href="https://lnkd.in/gCP4GAhs">https://lnkd.in/gCP4GAhs</a></p>
<p>You can find out a bit more about the Minderoo OceanOmics Centre at UWA here: <a href="https://lnkd.in/gmXKjXNu">https://lnkd.in/gmXKjXNu</a></p>
<p>And the broader Minderoo OceanOmics program here: <a href="https://lnkd.in/gtKHSk7g">https://lnkd.in/gtKHSk7g</a></p>
<p>Or get in touch if you want to know more!</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-37579490864269040582022-10-21T15:07:00.004+11:002022-10-26T19:37:16.528+11:00The Ocean Genomes Lab is hiring - Bioinformatics and Sequencing technicians wanted!<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEtuZSCUOOyOY71gBwAOC19zZZZnt1yyrWeaxclOHxQwvo19bXDp1WRXNyNzih5wcYoyfOMrlyubjMXIRwFF3fTkUXyoQUM7H19lRvsu__cbALkEMDlypUuPYSXFaTArfiw8qtRUxUUSyawibC9BtZLsoz_IAZna-gRg3tvV_9jqR2wFBZMy-V63y5/s600/OGL-button.png" style="display: block; padding: 1em 0; text-align: center; clear: right; float: right;"><img alt="" border="0" width="150" data-original-height="600" data-original-width="600" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEtuZSCUOOyOY71gBwAOC19zZZZnt1yyrWeaxclOHxQwvo19bXDp1WRXNyNzih5wcYoyfOMrlyubjMXIRwFF3fTkUXyoQUM7H19lRvsu__cbALkEMDlypUuPYSXFaTArfiw8qtRUxUUSyawibC9BtZLsoz_IAZna-gRg3tvV_9jqR2wFBZMy-V63y5/s320/OGL-button.png"/></a>
<p>Adding to the <a href="http://edwardslab.blogspot.com/2022/10/the-ocean-genomes-laboratory-is-hiring.html">recently advertised Sequencing technician posts</a> (closing 27 October), we are now pleased to advertise <strong><a href="https://external.jobs.uwa.edu.au/cw/en/job/512865">two bioinformatics research assistant positions</a></strong> to support our creation of marine vertebrate reference genome library. If you have experience with genome assembly or bioinformatics workflows, and are passionate about saving marine biodiversity, come and join us!</p>
<p>Two positions are available at Level 5 or 6, depending on your experience. Both roles will be providing bioinformatics support for our marine vertebrate reference genome project. You’ll get to play with data from the latest sequencing toys, including Illumina NovaSeq 6000, NextSeq 2000 and iSeq 100, the PacBio Sequel IIe, and ONT (probably PromethION and MinION).</p>
<p>Job roles will include developing and applying genome assembly workflows, data curation and QC, data sharing, and development/benchmarking of comparative genomics and genome assembly curation tools. If you have experience or passion for integrating bioinformatics workflows with Laboratory Information Management Systems and/or Electronic Laboratory Notebooks, we’d also love to hear to from you. SQL database skills would not go amiss too.</p>
<p>We’re a new team with lots to do, so there is plenty of scope to make the position your own and play to your strengths.</p>
<p>The closing date for applications is <strong>11:55 PM AWST on Thursday 10 November 2022</strong>.</p>
<p>To learn more about these opportunities, please <a href="https://external.jobs.uwa.edu.au/cw/en/job/512865" target="_blank">click here</a> or contact Rich Edwards at rich.edwards@uwa.edu.au.</p>
<h2 id="abouttheteam">ABOUT THE TEAM</h2>
<p>The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and Computational Biology Services.</p>
<p>Equipped with the latest high-throughput sequencing technology and in collaboration with global partners, the Ocean Genomes Laboratory will generate a comprehensive library of high quality marine vertebrate reference genome assemblies. All such reference genome data will be subject to rigorous QA/QC and all assemblies will be released publicly with open access.</p>
<p>The Ocean Genomes Laboratory will undertake research and development under the direction of Minderoo’s ambitious OceanOmics Program which has the goal of revolutionising ocean conservation through novel marine sampling and genomics approaches and scaling these to significantly advance our knowledge of marine life. The Ocean Genomes Laboratory and Computational Biology Services will include state of the art infrastructure including sample and eDNA preparation areas, flow cytometry, single cell sequencing equipment and the latest bioinformatics and computational biology tools.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-26016025185370831962022-10-06T20:06:00.009+11:002022-11-25T19:24:30.597+11:00The Ocean Genomes Laboratory is hiring!<div class="separator" style="clear: both;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEtuZSCUOOyOY71gBwAOC19zZZZnt1yyrWeaxclOHxQwvo19bXDp1WRXNyNzih5wcYoyfOMrlyubjMXIRwFF3fTkUXyoQUM7H19lRvsu__cbALkEMDlypUuPYSXFaTArfiw8qtRUxUUSyawibC9BtZLsoz_IAZna-gRg3tvV_9jqR2wFBZMy-V63y5/s600/OGL-button.png" style="display: block; padding: 1em 0; text-align: center; clear: right; float: right;"><img alt="" border="0" width="200" data-original-height="600" data-original-width="600" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEtuZSCUOOyOY71gBwAOC19zZZZnt1yyrWeaxclOHxQwvo19bXDp1WRXNyNzih5wcYoyfOMrlyubjMXIRwFF3fTkUXyoQUM7H19lRvsu__cbALkEMDlypUuPYSXFaTArfiw8qtRUxUUSyawibC9BtZLsoz_IAZna-gRg3tvV_9jqR2wFBZMy-V63y5/s320/OGL-button.png"/></a></div>The Minderoo OceanOmics Centre at UWA Ocean Genomes Laboratory is now hiring our technical team to support high throughput DNA sequencing and genome assembly. We currently have three "wet" lab positions going: a <a href="https://www.seek.com.au/job/58643634?type=standard" target="_blank">Sequencing Specialist Scientific Officer</a>, and two <a href="https://www.seek.com.au/job/58690009?type=standard" target="_blank">Sequencing Technician</a> positions. Both roles will be providing technical support in the lab, particularly with respect to all aspects of DNA sequencing (sample extraction, library preparation and setting up sequencing runs). You'll get to play with the latest sequencing toys, including Illumina NovaSeq 6000, NextSeq 2000 and iSeq 100, the PacBio Sequel IIe, and ONT (probably PromethION and MinION).
<p>The <strong>closing date for applications is 11:55 PM AWST on Thursday 27 October 2022</strong>.</p>
<p>To learn more about these opportunities, please click on the links above or contact Rich Edwards at rich.edwards@uwa.edu.au. We will also be advertising some bioinformatics positions soon.</p>
<h2 id="abouttheteam">About the team</h2>
<p>The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and Computational Biology Services.</p>
<p>Equipped with the latest high-throughput sequencing technology and in collaboration with global partners, the Ocean Genomes Laboratory will generate a comprehensive library of high quality marine vertebrate reference genome assemblies. All such reference genome data will be subject to rigorous QA/QC and all assemblies will be released publicly with open access.</p>
<p>The Ocean Genomes Laboratory will undertake research and development under the direction of Minderoo’s ambitious OceanOmics Program which has the goal of revolutionising ocean conservation through novel marine sampling and genomics approaches and scaling these to significantly advance our knowledge of marine life. The Ocean Genomes Laboratory and Computational Biology Services will include state of the art infrastructure including sample and eDNA preparation areas, flow cytometry, single cell sequencing equipment and the latest bioinformatics and computational biology tools.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-64857778570923150242022-08-08T11:01:00.004+10:002022-10-21T15:13:24.071+11:00Senior Postdoc wanted for UWA Ocean Genomes Lab! (Closing soon)<p>The new Ocean Genomes Laboratory (part of the <a href="https://www.minderoo.org/oceanomics/" target="_blank">Minderoo OceanOmics</a> Centre at the <a href="https://www.uwa.edu.au/oceans-institute" target="_blank">UWA Oceans Institute</a>) is hiring a <a href="https://external.jobs.uwa.edu.au/en/job/509270/research-fellow-ocean-omics-laboratory" target="_blank">Level B postdoc in marine genomics</a>. (Three-year fixed term full time role, or flexible working equivalent.)</p>
<p>This is a rare opportunity to work as part of a collaborative team in a high-profile state of the art genomics research facility dedicated to studying marine vertebrates. You should have a PhD in bioinformatics, computational biology, molecular genetics or genomics, plus an interest in marine vertebrates and postdoctoral experience in high throughput DNA sequencing and whole genome assembly. The lab is new and there is plenty of scope to shape its direction beyond the core mission creating a marine vertebrate reference genome library as part of the <a href="https://vertebrategenomesproject.org/" target="_blank">Vertebrate Genome Project</a>. You will also have an important role in helping to supervise the lab staff and research team.</p>
<center><p style="color:red"><big><b>Closing date: 11:55pm AWST, Friday 12 August 2022</b></big></p></center>
<p>Please <a href="https://external.jobs.uwa.edu.au/en/job/509270/research-fellow-ocean-omics-laboratory" target="_blank">see the UWA job advert for more details</a>.
<h2>About the team</h2>
<p>The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and a Computational Biology Program.</p>
<p>Equipped with the latest high-throughput sequencing technology, and in collaboration with global partners, the Ocean Genomes Laboratory will generate a comprehensive library of high-quality marine vertebrate reference genome assemblies. All reference genome data will be subject to rigorous QA/QC and all assemblies will be released publicly through open access.</p>
<p>The OceanOmics Centre will be located in the Bayliss Building on the UWA Crawley Campus, OceanOmics staff sharing the building with research and teaching staff primarily from the UWA School of Molecular Sciences and interacting with staff in the UWA Oceans Institute in the nearby IOMRC building.</p>
<h2>About the opportunity</h2>
<p>As a Research Fellow you will join a research group committed to applying modern molecular biological methods to marine research.</p>
<p>Using modern genomic approaches, you will undertake research on marine vertebrates, focussed on the production, QC and assembly of high-quality reference genome data. You will participate in the entire workflow from sample collection and processing, generating genomic sequence data in the laboratory using multiple modern genome sequencing technologies, with a focus on data processing, assembly, curation, analysis and dissemination.</p>
<p>In this unique role you will also be supported to develop your leadership skills. Working closely with the Centre’s UWA Principal Research Fellow, junior postdoctoral academics, the Centre’s Laboratory Manager, and diverse researchers from Minderoo Foundation you will contribute to decision making, oversee the work of technicians and PhD students and provide leadership in modern high-quality genome assembly production and publication.</p>
Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-71968936485068218942022-07-22T15:40:00.000+10:002022-10-21T15:13:24.072+11:00The Edwards Lab is moving to the UWA Oceans Institute!<div class="separator" style="clear: both;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgj-y9gw4t6gBQQUnZqT67tPdxa_yf5Ut8mRHy81rcm2vGSNXuSwYB3481Kn_UHTISIJWz5qJYh2x4VrahX0IOIlF_JnGGl3KYuhkor9FWsJGYiAZGdoc3MGDojZhtkm0jr5GkoHUq3QkwOS9CHjcoPQf-l-f3jUoS8wqQmpxSb2rRCYTgnUAfBmwlg/s570/UWAOI.png" style="display: block; padding: 1em 0; text-align: center; clear: right; float: right;"><img alt="" border="0" width="265" data-original-height="136" data-original-width="570" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgj-y9gw4t6gBQQUnZqT67tPdxa_yf5Ut8mRHy81rcm2vGSNXuSwYB3481Kn_UHTISIJWz5qJYh2x4VrahX0IOIlF_JnGGl3KYuhkor9FWsJGYiAZGdoc3MGDojZhtkm0jr5GkoHUq3QkwOS9CHjcoPQf-l-f3jUoS8wqQmpxSb2rRCYTgnUAfBmwlg/s200/UWAOI.png"/></a></div><p>More details will follow but, in August, I will be starting a new position at the <a href="https://www.uwa.edu.au/oceans-institute">University of Western Australia Oceans Institute</a> to head up the new Ocean Genomes Laboratory as part of the <a href="https://www.minderoo.org/oceanomics/">Minderoo OceanOmics</a> Centre. This exciting project will collaborate closely with the Minderoo Foundation, the <a href="https://vertebrategenomesproject.org/">Vertebrate Genome Project</a>, and scientists across Australia to create marine vertebrate reference genomes.</p>
<p>The goal of the Ocean Genomes Lab is "building and openly publishing the reference libraries for marine vertebrates ... to accurately detect, monitor and determine the health of these species". The lab is still being setup and we're hiring. Currently available is a Level B postdoc positions: <a href="http://bit.ly/OceanOmics">http://bit.ly/OceanOmics</a>. If building genomes is your thing, and you want to help fight the biodiversity crisis in our oceans, come and work with me! (Or pass it on if you know someone who does!) Research Assistant positions will follow.</p>
<p>Look out for a bunch of updates over the next few weeks, both as I update some of the outstanding presentations and posters from this year, and as the website rebrands. In the meantime, please get in touch if any of this sounds interesting!</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-58053351230141321212022-02-13T13:00:00.003+11:002022-02-13T15:02:33.016+11:00Edwards Lab at #LorneGenome 2022<p><a href="https://www.lornegenome.org/program">Lorne Genome 2022</a> (the 43rd Annual Lorne Genome Conference 2022) kicks off today in Lorne and online. I wasn’t able to make it in person this year due to Omicron and teaching commitments, but happily the lab is still well represented. As well as an online talk, we have two in-person posters, so please check these out if you are lucky enough to be attending in the flesh.</p>
<ul>
<li><strong>Poster #138:</strong> Stephanie H Chen. <a href="#chen138">A chromosome-level reference genome for <em>Telopea speciosissima</em> (New South Wales waratah) provides insight into waratah evolution.</a> [Sunday 13th Poster Session]</li>
<li><strong>Talk #17</strong>. Richard Edwards. <a href="#edwards17">Small but mitey: high-quality long-read assembly of a streamlined mite genome from contaminated sequencing data.</a> [Monday 14th, Session 3A - Computational Biology and Bioinformatics]</li>
<li><strong>Poster #255:</strong> Katarina C Stuart. <a href="#stuart255">A genetic perspective on rapid adaptation in the globally invasive European starling (<em>Sturnus vulgaris</em>).</a> [Monday 14th Poster Session]</li>
</ul>
<p>Details below.</p>
<a name="chen138"><hr /></a>
<h2>A chromosome-level reference genome for Telopea speciosissima (New South Wales waratah) provides insight into waratah evolution (#138)</h2>
<p><strong><u>Stephanie H Chen</u>, Jason G Bragg, Richard J Edwards</strong></p>
<a href="https://blogger.googleusercontent.com/img/a/AVvXsEhTkdTcgEHEX4gmjR80iH5iWkgDTwWykzfA2_LnjPHxydX5Gw3iJVMIPsKB47MAh83ejKFAgn2oigYT94dkUNAMghStroQwxDr9qqD-sYcOcP1KLkxZPd3wQXiFoh2W0dGIH8BffF2jZO1m_nT8300XSd3UOuPSqmJwbYxLx9ZZlsBn7YBrwbEeuxY8=s3508" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="" border="0" width="280" data-original-height="3508" data-original-width="2483" src="https://blogger.googleusercontent.com/img/a/AVvXsEhTkdTcgEHEX4gmjR80iH5iWkgDTwWykzfA2_LnjPHxydX5Gw3iJVMIPsKB47MAh83ejKFAgn2oigYT94dkUNAMghStroQwxDr9qqD-sYcOcP1KLkxZPd3wQXiFoh2W0dGIH8BffF2jZO1m_nT8300XSd3UOuPSqmJwbYxLx9ZZlsBn7YBrwbEeuxY8=s320"/></a>
<p><em>Telopea</em> is an eastern Australian genus of five species of long-lived shrubs in the family Proteaceae. Previous work has characterised population structure and patterns of introgression between <em>Telopea</em> species. These studies were performed using a limited set of genetic markers, but point to the great potential of waratah as a model clade for understanding the processes of divergence, environmental adaptation and speciation, when enhanced by a genome-wide perspective enabled by a reference genome. However, few Proteaceae genomes and no waratah genomes are available.</p>
<p>We assembled the first chromosome-level reference genome for <em>T. speciosissima</em> (New South Wales waratah; 2n = 22) using Nanopore long-reads, 10x Chromium linked-reads and Hi-C data. The assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8 % of Embryophyta universal single-copy orthologues (BUSCOs; n = 1,614) complete. Read depth analysis of 140 ‘Duplicated’ BUSCO genes reveals that almost all are real duplications, increasing confidence in protein family analysis using annotated protein-coding genes, highlighting a possible need to revise the BUSCO set for this lineage. Genome annotation predicted 34,706 genes and pseudogenes, including 27,481 protein-coding genes. We examined the evolutionary dynamics of <em>Telopea</em> using the reference genome in conjunction with DArTseq (n = 244) and whole genome shotgun sequencing (n = 14) of each of the seven lineages; there are three lineages of <em>T. speciosissima</em> – coastal, upland and southern.</p>
<p>Here, I will discuss the population structure and demographic history of the genus. We also examined phylogenomic relationships and developed a scalable method of rapidly generating species trees from short-read data to maximise the recovery of informative data from genomic datasets. The waratah reference genome represents an important new genomic resource in Proteaceae to accelerate our understanding of the origins and evolutionary dynamics of the Australian flora.</p>
<p>[Read more about the waratah genome, <a href="http://edwardslab.blogspot.com/2022/01/the-waratah-genome-paper-is-out.html">here</a>.]</p>
<a name="edwards17"><hr /></a>
<h2>Small but mitey: high-quality long-read assembly of a streamlined mite genome from contaminated sequencing data (#17)</h2>
<p><strong><u>Richard J Edwards</u>, Stephanie H Chen, Jason G Bragg.</strong></p>
<a href="https://blogger.googleusercontent.com/img/a/AVvXsEgMRhEduwcezIljZCQibs2Z8XIEhuaHHdST4udnvY2_bFM8Y_JpzWvZNntMgGyMTOF1XGj8HsSD8WXv5LZMbsoNBqbdi_HOlXc1drKEItRnBDXDkt6KyjV2PS5XSJ2824yLLnF0Rf6nBTXOGidEpJbcctDQnQJMa47J1vB9rkoxw-Z0eK1uSAoIlnmp=s1200" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="" border="0" width="320" data-original-height="675" data-original-width="1200" src="https://blogger.googleusercontent.com/img/a/AVvXsEgMRhEduwcezIljZCQibs2Z8XIEhuaHHdST4udnvY2_bFM8Y_JpzWvZNntMgGyMTOF1XGj8HsSD8WXv5LZMbsoNBqbdi_HOlXc1drKEItRnBDXDkt6KyjV2PS5XSJ2824yLLnF0Rf6nBTXOGidEpJbcctDQnQJMa47J1vB9rkoxw-Z0eK1uSAoIlnmp=s320"/></a>
<p>As pilot data for project on myrtle rust resistance, we previously assembled two Myrtaceae genomes using 10x Chromium linked reads: <em>Rhodamnia argentea</em> (silver malletwood) and <em>Syzygium oleosum</em> (blue lilly pilly). Both draft genomes achieved scaffolding (N50 > 850 kb) and completeness (BUSCOv3 embryophyta_odb9 > 90 %) of sufficient quality to be annotated by NCBI RefSeq. However, signs of arthropod sequence contamination were subsequently found in the <em>Rhodamnia argentea</em> assembly. We therefore sought to identify and eliminate this contamination during improvement and curation of the genome for publication.</p>
<p>A risk-averse analysis highlighted 49.6 Mb (11.95%) on 2,996 of 15,781 scaffolds of possible arthropod origin. An improved assembly of the same tree, incorporating ~50X long-read (ONT) sequencing, has confirmed this contamination as 11 scaffolds (34.6 Mb) that are distinct from 75 <em>R. argentea</em> assembly scaffolds (346.7 Mb), increasing the likelihood of contamination over the integration of horizontally transferred genes. Taxonomic analysis of predicted protein-coding genes using Taxolotl (<a href="https://github.com/slimsuite/taxolotl">https://github.com/slimsuite/taxolotl</a>) suggested that the contamination most likely originates from some form of mite (Order: Trombidiformes), but limited NCBInr mite sequences precluded better taxonomic resolution. Curiously, these contamination scaffolds showed a high depth of coverage (~36X), but a fairly low BUSCO completeness of 58.1% (v5 Augustus, metazoa_odb10 n=954), apparently inconsistent with typical mite genomes.</p>
<p>Phylogenomic analysis with available mite genomes identified the closest relative as Aculops lycopersici, a microscopic (0.2 mm long) eriophyoid mite with a heavily streamlined 32.5 Mb genome. Original low completeness appears to be from a combination of genome reduction and poor performance of that BUSCO version; BUSCO v5 MetaEuk eukaryota_odb10 (n=255) reports 82.8% completeness, which is approaching the 86.3% of <em>A. lycopersici</em>. Here, we discuss the evidence that we have assembled a highly complete but streamlined genome from an unknown eriophyoid mite, plus the need to improve genomic representation of contaminating pest species.</p>
<a name="stuart255"><hr /></a>
<h2>A genetic perspective on rapid adaptation in the globally invasive European starling (Sturnus vulgaris) (#255)</h2>
<p><strong><u>Katarina C Stuart</u>, Richard J Edwards, William (Bill) B Sherwin, Lee Ann Rollins.</strong></p>
<a href="https://blogger.googleusercontent.com/img/a/AVvXsEhC3gACT8f1auHLoYZwxwvLc0rp4Mzp-donC_juIoejhhK3liH_WyrlyytjvCF9DAwT53dbRuZwKXmwP5ZNKLCQALZ1r0gay_kOzuifWd2cU7549n1Us2DUWoqWws4MRu0l1pvUvAHUWAikmQxjlw5ZzFcvhQxFDksM9jtdlzkiiaEztoWv-4nSl8pX=s3507" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="" border="0" height="280" data-original-height="3507" data-original-width="2483" src="https://blogger.googleusercontent.com/img/a/AVvXsEhC3gACT8f1auHLoYZwxwvLc0rp4Mzp-donC_juIoejhhK3liH_WyrlyytjvCF9DAwT53dbRuZwKXmwP5ZNKLCQALZ1r0gay_kOzuifWd2cU7549n1Us2DUWoqWws4MRu0l1pvUvAHUWAikmQxjlw5ZzFcvhQxFDksM9jtdlzkiiaEztoWv-4nSl8pX=s320"/></a>
<p>Few invasive birds are as globally successful or as well-studied as the common starling (<em>Sturnus vulgaris</em>). Native to the Palaearctic, the starling has been a prolific invader in North and South America, southern Africa, Australia, and The Pacific Islands, while facing declines in excess of 50% in in some native regions. Starlings present an invaluable opportunity to test predictions about the evolutionary trajectory of invasive populations, and gain insight into genetic shifts in response to anthropogenic alteration and climate change.</p>
<p>My research focuses primarily on the invasive European starling population in Australia and aims to investigate the genetics underlying their evolution, using a range of genomic approaches. Through historic museum sample sequencing, I examine single nucleotide polymorphism variations shifts between the native range and Australia, and find parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants and carbohydrate exposure. I further examine matched genetic, morphological, and environmental data to reveal patterns of heritability and plasticity across ecologically significant phenotypic traits, revealing that elevation, as well as rainfall and temperature variability plays an important role in shaping morphology and genetics. Finally, I investigated patterns of structural variants, to uncover evolutionarily significant large-scale genetic variants across a global data set, and more specifically characterise their role in rapid starling adaptation across the entirety of the Australian range. Overall, my research seeks to better understand mechanisms and patterns of genetic change within this species, which may be used to inform invasion or native range management. More broadly, this evolutionary research into the starling provide an important perspective on the role of rapid evolution in invasive species persistence, and the global pressures that may shape range shifts and evolution across many similar avian taxa.</p>
Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-39157099887699023352022-01-25T22:19:00.002+11:002022-01-25T22:19:35.842+11:00Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes<p>The first of the <a href="https://babsgenome.blogspot.com/">BABS Genome</a> papers has finally arrived, featuring our <a href="http://edwardslab.blogspot.com/2018/06/sequencing-snakes-pseudodiploid-pseudo.html">two 10x Genomics Supernova snake genomes</a>. Such is the speed that genomics is moving, the snake assemblies themselves have moved on quite a bit since then and we hope to release chromosome-level versions soon. (The goalposts for a genome paper moved faster than they could be written up - always a challenge without dedicated researchers working on assemblies! Do get in touch if they’d be useful and we can collaborate.) </p>
<p><a href="https://www.mdpi.com/genes/genes-13-00217/article_deploy/html/images/genes-13-00217-g004-550.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="" border="0" width="320" data-original-height="550" data-original-width="532" src="https://www.mdpi.com/genes/genes-13-00217/article_deploy/html/images/genes-13-00217-g004-550.jpg"/></a>Rather than a pure genome paper, this paper makes use of our two elapid genomes to ask some interesting questions about possible horizontal transfer of transposable (mobile genetic) elements during the evolution of sea snakes - our two elapids provided good sister (mainland tiger snake) and outgroup (eastern brown snake) taxa for the olive sea snake, which was the focus of the study. It was doubly pleasing to collaborate on a transposable elements paper, as they were the subject of my PhD (albeit in bacteria, see <a href="http://edwardslab.blogspot.com/2002/05/a-simple-method-for-genome-wide.html">here</a> and <a href="http://edwardslab.blogspot.com/2003/01/transiently-beneficial-insertions-could.html">here</a>).</p>
<p>This paper is part of a special issue, <a href="https://www.mdpi.com/journal/genes/special_issues/Phylogenomic_Reconstructions">Mobile Elements in Phylogenomic Reconstructions</a>, and features some interesting examples of probable horiztonal transfer of mobile elements that provide insights into the evolutionary history of these species.</p>
<hr>
<p><b>Galbraith JD, Ludington AJ, Sanders KL, Amos TG, Thomson VA, Enosi Tuipulotu D, Dunstan N, <u>Edwards RJ</u>, Suh A, Adelson DL (2022):</b> Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes. <i>Genes</i> <b>13(2)</b>:217.
[<a href="https://doi.org/10.3390/genes13020217">Genes</a>]
[<a href="https://www.mdpi.com/2073-4425/13/2/217/pdf">PDF</a>]
[<a href="https://www.biorxiv.org/content/10.1101/2021.06.22.449521v1">bioRxiv</a>]
</p>
<h2 id="abstract">Abstract</h2>
<blockquote>
<p>Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo–Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~30 Mya and have since rapidly diversified into six amphibious, ~60 marine and ~100 terrestrial species that fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.</p>
</blockquote>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-79860059210809361442022-01-14T22:06:00.003+11:002022-01-14T22:06:23.176+11:00The Waratah genome paper is out!<p><a href="https://pbs.twimg.com/media/FI3o8t-aIAAGo3E?format=jpg&name=medium" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="" border="0" width="320" data-original-height="800" data-original-width="800" src="https://pbs.twimg.com/media/FI3o8t-aIAAGo3E?format=jpg&name=medium"/></a>
The final version of the waratah genome paper now out in <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13574">Molecular Ecology Resources</a>. This was a fun collaboration with the Royal Botanic Gardens and Domain Trust as <a href="http://edwardslab.blogspot.com/2018/12/what-are-we-sequencing-next-waratah.html">one of the pilot genomes for BioPlatforms Australia’s Genomics for Australian Plants (GAP) initiative</a>.</p>
<p>You can read the press release <a href="http://unsw.to/waratahgenome">here</a>, or our piece in the Conversation, <a href="https://theconversation.com/weve-unveiled-the-waratahs-genetic-secrets-helping-preserve-this-australian-icon-for-the-future-174772"><strong>We’ve unveiled the waratah’s genetic secrets, helping preserve this Australian icon for the future</strong></a>.</p>
<p>In this paper, we present a chromosome-level assembly for the NSW State Floral Emblem, the New South Wales waratah, <i>Telopea speciosissima</i>. This joins macadamia as the 2nd reference genome for the Proteaceae family & should help future studies for the remaining ca. 1700 species.</p>
<p>The genome was assembled from a ONT chassis, scaffolded with 10x Genomics linked reads and Phase Genomics HiC - made possible thanks to quality data from AGRF and the Ramaciotti Centre for Genomics. The final assembly was chromosome-level, with 94.1% on the 11 chromosomes (<i>2n</i> = 22).</p>
<p>As well as the assembly itself, the paper presents a three genomics tools that we hope will be helpful for other assemblies:</p>
<p>1. <b><a href="https://github.com/slimsuite/depthsizer">DepthSizer</a></b> uses long-read depths and BUSCO predictions to estimate genome size. We estimated the waratah genome to be ca. 900 Mbp - bigger than kmer estimates, but smaller than flow cytometry of Tasmanian waratah.</p>
<p><a href="https://github.com/slimsuite/depthsizer" style="margin-bottom: 1em; margin-top: 1em;"><img alt="" border="0" width="284" src="https://pbs.twimg.com/media/FI3toL-acAM3sRy?format=jpg&name=small"/></a>
<a href="https://github.com/slimsuite/depthsizer" style="margin-bottom: 1em; margin-top: 1em;"><img alt="" border="0" width="284" src="https://pbs.twimg.com/media/FI3wc8aaMAciSgw?format=jpg&name=900x900"/></a></p>
<p>2. <b><a href="https://github.com/slimsuite/diploidocus">Diploidocus</a></b> builds on Purge Haplotigs, combining read depths, kmer frequencies & BUSCO predictions to classify and curate/filter assembly scaffolds. This decreases false duplications & contamination, and flags collapsed repeats for closer inspection.</p>
<p><a href="https://github.com/slimsuite/diploidocus" style="margin-bottom: 1em; margin-top: 1em;"><img alt="" border="0" width="568" src="https://pbs.twimg.com/media/FI3wiB0acAQKFxc?format=jpg&name=900x900"/></a></p>
<p>3. <b><a href="https://github.com/slimsuite/depthkopy">DepthKopy</a></b> uses BUSCO Complete genes to establish sequencing depth (like DepthSizer) and then estimates copy number for regions (e.g. genes), scaffolds & sliding windows of the assembly. This showed that most “Duplicated” BUSCOs are real duplicates.</p>
<p><a href="https://github.com/slimsuite/depthkopy" style="margin-bottom: 1em; margin-top: 1em;"><img alt="" border="0" width="568" src="https://pbs.twimg.com/media/FI3wTHsaMAEBqRP?format=jpg&name=medium"/></a></p>
<hr>
<p><b>Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JS, Sauquet H, Bourke G, Amos TG, Bragg JG & <U>Edwards RJ</U> (accepted):</b> <a href="http://edwardslab.blogspot.com/2021/06/chromosome-level-de-novo-genome.html" target="_blank">Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C</a>. <i>Molecular Ecology Resources</i>. <br />
[<a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13574">Mol Ecol Res</a>]
[<a href="https://doi.org/10.1101/2021.06.02.444084">bioRxiv</a>]</p>
<h2 id="abstract">Abstract</h2>
<blockquote>
<p><i>Telopea speciosissima</i>, the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for <i>T. speciosissima</i>. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8% of Embryophyta BUSCOs “Complete”. We present a new method in Diploidocus (<a href="https://github.com/slimsuite/diploidocus">https://github.com/slimsuite/diploidocus</a>) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (<a href="https://github.com/slimsuite/depthsizer">https://github.com/slimsuite/depthsizer</a>), for genome size estimation from the read depth of single-copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1% of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA (CYC) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 “Duplicated” BUSCO genes using a new tool, DepthKopy (<a href="https://github.com/slimsuite/depthkopy">https://github.com/slimsuite/depthkopy</a>), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level <i>T. speciosissima</i> reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.</p>
</blockquote>
<p>If you want a read and don’t have access, please get it touch or check out the <a href="https://doi.org/10.1101/2021.06.02.444084">bioRxiv preprint</a>.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-83080879174031825472022-01-12T16:30:00.015+11:002022-01-14T23:14:03.930+11:00SLiMSuite & SeqSuite sequence analysis tools: SLiMSuite release v1.11.0 (2022-01-12)<p>SLiMSuite has (finally!) been updated in line with the recent waratah genome paper. See the SLiMSuite blog for more details:</p>
<p><a href="https://doi.org/10.5281/zenodo.5839162"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.5839162.svg" alt="DOI"></a></p>
<p><a href="https://slimsuite.blogspot.com/2022/01/slimsuite-release-v1110-2022-01-12.html?spref=bl">SLiMSuite & SeqSuite sequence analysis tools: SLiMSuite release v1.11.0 (2022-01-12)</a></p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-55075080033853605272021-12-03T10:28:00.007+11:002022-01-26T10:59:18.564+11:00Limited Introgression between Rock-Wallabies with Extensive Chromosomal Rearrangements<p>When we were assembling the 10x Genomics linked read assemblies of several rock wallabies, one of them <a href="http://edwardslab.blogspot.com/2019/01/we-have-new-10x-supernova-assembly-lab.html">broke the lab record for Supernova assembly quality</a>.</p>
<p><a href="https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab333/6448774" style="display: block; padding: 1em 0; text-align: center; clear: right; float: right; margin-left: 10px;"><img alt="" align="center" border="0" width="260" data-original-height="341" data-original-width="520" src="https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/mbe/PAP/10.1093_molbev_msab333/2/m_msab333f1.jpeg?Expires=1642094682&Signature=QUQkxIr5GdPegFEdksUU4FPU7kX3MFRiUg~7LhXQ5Y6W28AnLetAgMnzFXN3smrrwMhR78o-L1g088naXetDtbgOwpEu57R3swtv0PbmyaShXTuYuCxG0d5trd~G-KggHIjU074V0dpDFNNEcHNP04fiZcqyBxRANen0QFvZM1DWTg-pzK33NrinMf7lQPtpjH0uiQV2pe9vVeU5B7kX0YNokmzUqoqJ0tPmejwxakHIZSIeTKPMxwnp0OkG3b8Oiuh4yGYKDo2w0QnJ8fVFMfBOIJaL52m4zORDVs-Qzz4WY8gESgKg5ZMCUh1LFB1iH1zQBoNnE3d73fgxkdx5JA__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA"/></a>10x linked reads are a bit of a dead technology now, but genomes made with them are still useful and generating insights. One example is the first rock wallaby we assembled, as a (very small) part of a team that used the draft 10x genome assembly for <em>Petrogale penicillata</em> as a reference to investigate chromosomal rearrangements, <a href="https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab333/6448774">published online today in <em>Molecular Biology and Evolution</em></a>, one of my favourite journals.</p>
<hr>
<p><strong>Potter P, Bragg JG, Turakulov R, Eldridge MDB, Deakin J, Kirkpatrick M, <u>Edwards RJ</u> & Moritz C (2022):</strong> Limited introgression between rock-wallabies with extensive chromosomal rearrangements. <em>Molecular Biology and Evolution</em> <b>39(1):</b>msab333 <a href="https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab333/6448774">https://doi.org/10.1093/molbev/msab333</a></p>
<h2 id="abstract">Abstract</h2>
<blockquote>
<p>Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus <i>Petrogale</i>) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive sampling of populations and genomes of <i>Petrogale</i> from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in divergence, speciation, and patterns of molecular evolution.</p>
</blockquote>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-67505120111627480332021-12-02T09:41:00.004+11:002021-12-02T09:42:25.452+11:00EdwardsLab at Australasian Evolution Society #AUSEVO2021<p>Look out for some interesting talks by Edwards Lab members at this year’s <a href="https://ausevo.com/conference/">Australasian Evolution Society 2021 conference</a>, starting today: </p>
<p><strong>Thursday 2nd December: 3-minute talks | 1130-1230</strong></p>
<h2 id="keltoncheung-analysisofmitochondrialdnarevealssignificantgeneticdiversityininvasiveaustraliancanetoads">Kelton Cheung - Analysis of mitochondrial DNA reveals significant genetic diversity in invasive Australian cane toads</h2>
<p><u>Kelton Cheung</u>, Mark Richardson, Richard Edwards & Lee Ann Rollins</p>
<blockquote>
<p>Mitochondrial DNA haplotype patterns across the native and invaded ranges can reveal the history and evolutionary trajectory of invasions. The invasion of Australia by the cane toad (<i>Rhinella marina</i>) has accelerated as it expanded westward. Despite this success, previous studies reported no mitochondrial genetic diversity in Australia. Here, we assembled a complete mitochondrial reference genome and haplotyped toads (N=119) from the native range and two introduced populations (Hawai’i and Australia), using whole genome and RNA-seq data. The complete <i>R. marina</i> mitochondrial genome consists of 18,152 base pairs with no significant gene arrangement as compared to other bufonid species. Although native range genetic diversity was much higher than that of the introduced ranges, we identified 29 haplotypes in Australia. While we did find evidence of founder effects following introduction, our results suggest there is significant genetic diversity within Australia, which may assist adaptation and invasion success in this species. </p>
</blockquote>
<hr>
<p><strong>Thursday 2nd December: Selection 1 | 1415-1430</strong></p>
<h2 id="katarinastuart-ageneticperspectiveonrapidadaptationinthegloballyinvasiveeuropeanstarlingsturnusvulgaris">Katarina Stuart - A genetic perspective on rapid adaptation in the globally invasive European starling (Sturnus vulgaris)</h2>
<p><em>Abstract coming soon…</em></p>
<hr>
<p><b>Thursday 2nd December: Biogeography and phylogenetics | 1530-1545</b></p>
<h2 id="richardedwards-depthkopy:copynumberpredictionusingsingle-copylong-readdepthprofiles">Richard Edwards - DepthKopy: copy number prediction using single-copy long-read depth profiles</h2>
<p><u>Richard J Edwards</u>, Stephanie H Chen, Katarina C Stuart, Mark M Tanaka & Jason G Bragg</p>
<blockquote>
<p>Gene duplication, followed by functional divergence of gene copies, is a fundamental component of genetic adaption and the evolution of novelty. Increasingly, evolutionary studies make use of the ever-expanding number of high-quality genome assemblies to characterise patterns of gene gain and loss. However, even reference genomes of the highest quality can experience assembly errors at tandemly repeated gene loci, resulting in incorrect inference of gene duplication patterns. Here, we present DepthKopy (<a href="https://github.com/slimsuite/depthkopy">https://github.com/slimsuite/depthkopy</a>), which estimates the copy number for a gene, region or sequence of interest, using an estimate of single-copy sequencing depth derived from complete BUSCO genes. This is useful for identifying haplotigs, and collapsed repeat regions during genome assembly curation. Critically, for evolutionary studies of gene families, DepthKopy can identify genes for which the number of genes in the assembly does not seem to match the genome.</p>
</blockquote>
<hr>
<p><strong>Friday 3rd December: Climate change and temperature | 1330-1345</strong></p>
<h2 id="collinahrens-genomicconstraintsofdroughtadaptation">Collin Ahrens - Genomic constraints of drought adaptation</h2>
<p><em>Abstract coming soon…</em></p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-17510255106174910962021-11-24T11:13:00.003+11:002021-11-24T11:13:19.350+11:00#ABACBS2021 Lightning talk - DepthSizer and DepthKopy: genome size and copy number prediction using single-copy long-read depth profiles<p>Tune in for the <a href="https://www.abacbs.org/conference2021">ABACBS 2021</a> lightning talks this morning to hear about our applications of long reads to genome size and copy number prediction. For more information, you can read the <a href="https://www.biorxiv.org/content/10.1101/2021.06.02.444084v2">NSW Waratah genome paper pre-print</a> or visit the GitHub pages for <a href="https://github.com/slimsuite/depthsizer">DepthSizer</a> and <a href="https://github.com/slimsuite/depthkopy">DepthKopy</a>.</p>
<p><u>Richard J Edwards</u>, Stephanie H Chen, Katarina C Stuart, Mark M Tanaka, Jason G Bragg.</p>
<p><strong>DepthSizer and DepthKopy: genome size and copy number prediction using single-copy long-read depth profiles</strong></p>
<blockquote>
<p>A fundamental part of any genome project is establishing the genome size of the organism being sequenced. The gold standard for genome size measurement is flow cytometry, but this is not available to all groups and can give surprisingly variable results. Popular bioinformatic approaches predict genome size using kmer frequency profiles from high-accuracy (e.g. illumina or hifi) sequencing reads, or the mean depth of coverage reads mapped to an assembly. Both of these approaches can be adversely affected by repetitive regions of the genome. Mean sequencing depth is also highly reliant on assembly completeness.</p>
</blockquote>
<blockquote>
<p>Here, we present DepthSizer (https://github.com/slimsuite/depthsizer), which refines this approach by estimating sequencing depth based on single-copy complete BUSCO genes. DepthSizer works on the principle that genuine single-copy regions will tend towards the same, true, single-copy read depth. In contrast, assembly errors, collapsed repeats within those genes, or incorrect BUSCO predictions, will give inconsistent read depth deviations. The modal read depth across single-copy BUSCO genes, calculated from a depth density profile of these regions, should therefore provide a good estimate of the true depth of coverage. The method is benchmarked on model organism data and corrections for possible contamination, biases/inconsistencies in read mapping and/or raw read insertion/deletion error profiles are discussed. We also present DepthKopy (https://github.com/slimsuite/depthkopy), which uses the same read depth approach to estimate the copy number of assembly regions. This can be useful for identifying haplotigs, and collapsed repeat regions.</p>
</blockquote>
<p>Keywords: BUSCO, Genome Assembly, Genomics, ONT, PacBio, copy number variants</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-5774530127244709352021-10-11T17:52:00.009+11:002021-10-11T19:33:30.033+11:00SLiMSuite Short Linear Motif and Genomics Analysis Tools: BUSCOMP v0.13.0 (MetaEuk) release<p><a href="https://slimsuite.blogspot.com/2021/10/buscomp-v0130-metaeuk-release.html?spref=bl">SLiMSuite: BUSCOMP v0.13.0 (MetaEuk) release</a>: <a href="https://github.com/slimsuite/buscomp" target="_blank">BUSCOMP v0.13.0 is now on GitHub</a>. This release features updates to parse additional BUSCO v5 outputs, including transcriptome and proteome modes. It has also been updated to be compatible with MetaEuk runs by generating the missing <code>*.fna</code> files where possible.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-3997958160771943902021-10-11T10:27:00.007+11:002021-10-11T17:53:04.072+11:00Congratulations to the Edwards Lab #GSAA21 Award winners<p>Congratulations to <a href="http://edwardslab.blogspot.com/2018/02/katarina-stuart-phd-student.html">Katarina Stuart</a>, <a href="https://edwardslab.blogspot.com/2019/05/stephanie-chen-phd-student.html">Stephanie Chen</a>, and <a href="http://edwardslab.blogspot.com/2021/02/cadel-watson-honours-student.html">Cadel Watson</a>, who all won prizes at this year’s <a href="https://edwardslab.blogspot.com/2021/10/edwards-lab-at-genetics-society-of.html">Genetics Society of AustralAsia 2021 Conference</a>. </p>
<p>Stephanie’s abstract was selected for the Spencer Smith-White Travel Award, Katarina won the best student talk award, and Cadel won the best student lightning talk award. Well done, all!</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-25489508774050887612021-10-06T10:44:00.001+11:002021-10-11T10:20:10.238+11:00Edwards Lab at Genetics Society of AustralAsia 2021 #GSAA21<p>Look out for some interesting genomics talks by Edwards Lab members at this year’s <a href="https://genetics.org.au/2021-gsa-conference/" target="_blank">Genetics Society of AustralAsia 2021 conference</a>, which started today. Congratulation to Stephanie for winning the <strong>Spencer Smith-White Travel Award</strong> (shame about the lack of travel!), Cadel for getting a lightning talk as an Honours student. And a shout out to Kat, who is one of the conference organisers.</p>
<p><b>Thursday 7th October: Genomics and Transcriptomics Session | 1:30-2:00 (Lightning talks)</b></p>
<h2 id="cadelwatson-deduce:efficientidentificationofultraconservedelementsfrommultiplegenomes">Cadel Watson - dedUCE: efficient identification of Ultraconserved Elements from multiple genomes</h2>
<p><strong><u>Cadel Watson</U></strong>, Mitchell J. Cummins, Yasir Kusay, Maxine Halbheer, Eric Urng, John S. Mattick and <u>Richard J. Edwards</u></p>
<blockquote>
<p>Ultraconserved elements (UCEs) are DNA sequences which are extremely conserved and found almost unchanged in the genomes of multiple, divergent species [1]. UCEs have been found in a wide variety of organisms, including mammals, fish, insects, birds, and plants. Whilst the evidence suggests that that they are the result of natural selection, indicating biological importance, their function has thus far proven elusive [2]. The recent (and ongoing) explosion in the quality and quantity of reference genomes across multiple taxa provides new opportunities for investigating the prevalence, evolution and role of UCEs. However, the field is hampered by a lack of fast and resource-efficient algorithms to identify UCEs. Furthermore, common alignment-based algorithms fail to identify non-syntenic UCEs. </p>
<p>Here, we present dedUCE, a novel tool for identifying all UCEs in a set of genomes. dedUCE uses a hash-based algorithm to rapidly identify core UCE kmers that are shared by multiple genomes, before extending and merging candidates into a final comprehensive but non-redundant set of UCEs. dedUCE can support UCEs appearing out-of-order due to genetic rearrangements and/or assembly artefacts, and is able to return UCEs with inexact homology. Stringency can be controlled by parameters controlling the length, support (number of genomes) and required sequence identity. Preliminary results show that dedUCE can identify all UCEs in a group of 40 mammalian genomes in 8 hours on a 16-core machine, which is orders of magnitude faster than previous algorithms. Applications of dedUCE will be discussed, including improving the definition of UCEs, and making use of UCE content to assess genome assembly completeness. </p>
<ol>
<li><p>Gill Bejerano, Michael Pheasant, Igor Makunin, Stuart Stephen, W. James Kent, John S. Mattick, and David Haussler (2004). Ultraconserved El- ements in the Human Genome. Science, 304(5675):1321–1325. </p></li>
<li><p>Konstantinos Kritsas, Samuel E. Wuest, Daniel Hupalo, Andrew D. Kern, Thomas Wicker, and Ueli Grossniklaus (2012). Computational analysis and char- acterization of UCE-like elements (ULEs) in plant genomes. Genome Research, 22(12):2455–2466. </p></li>
</ol>
</blockquote>
<hr>
<p><b>Friday 8th October: Ecological and Evolutionary Genetics Session | 10:45-11:00</b></p>
<h2 id="katarinastuart-ageneticperspectiveonrapidadaptationinthegloballyinvasiveeuropeanstarlingsturnusvulgaris">Katarina Stuart - A genetic perspective on rapid adaptation in the globally invasive European starling (Sturnus vulgaris)</h2>
<p><strong><u>Stuart KC</u></strong>, Sherwin WB, <u>Edwards RJ</u> & Rollins LA</p>
<blockquote>
<p>Few invasive birds are as globally successful or as well-studied as the common starling (<i>Sturnus vulgaris</i>). Native to the Palaearctic, the starling has been a prolific invader in North and South America, southern Africa, Australia, and The Pacific Islands, while facing declines in excess of 50% in in some native regions. Starlings present an invaluable opportunity to test predictions about the evolutionary trajectory of invasive populations, and gain insight into genetic shifts in response to anthropogenic alteration and climate change. My research focuses primarily on the invasive European starling population in Australia and aims to investigate the genetics underlying their evolution, using a range of genomic approaches. Through historic museum sample sequencing, I examine single nucleotide polymorphism variations shifts between the native range and Australia, and find parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants and carbohydrate exposure. I further examine matched genetic, morphological, and environmental data to reveal patterns of heritability and plasticity across ecologically significant phenotypic traits, revealing that elevation, as well as rainfall and temperature variability plays an important role in shaping morphology and genetics. Finally, I investigated patterns of structural variants, to uncover evolutionarily significant large-scale genetic variants across a global data set, and more specifically characterise their role in rapid starling adaptation across the entirety of the Australian range. Overall, my research seeks to better understand mechanisms and patterns of genetic change within this species, which may be used to inform invasion or native range management. More broadly, this evolutionary research into the starling provide an important perspective on the role of rapid evolution in invasive species persistence, and the global pressures that may shape range shifts and evolution across many similar avian taxa.</p>
</blockquote>
<hr>
<p><b>Friday 8th October: Spencer Smith-White Travel Award recipient | 1:15-1:30</b></p>
<h2 id="stephaniechen-genomicsofspeciationandintrogression:insightsfromwaratahtelopeaspp.asamodelclade">Stephanie Chen - Genomics of speciation and introgression: insights from waratah (Telopea spp.) as a model clade</h2>
<blockquote>
<p>Telopea is an eastern Australian genus of five species of long-lived shrubs in the family Proteaceae. Previous work has characterised population structure and patterns of introgression between Telopea species. These studies were performed using a limited set of genetic markers, but point to the great potential of waratah as a model clade for understanding the processes of divergence, environmental adaptation and speciation, when enhanced by a genome-wide perspective enabled by a reference genome. However, few Proteaceae genomes and no waratah genomes are available. We assembled the first chromosome-level reference genome for <i>T. speciosissima</i> (New South Wales waratah; 2n = 22) using Nanopore long-reads, 10x Chromium linked-reads and Hi-C data. The assembly spans 823 Mb, representing 93.9 % of the estimated genome size, with a scaffold N50 of 69.1 Mb and 91.3 % of complete Embryophyta universal single-copy orthologs (BUSCOs) are present. We examined the evolutionary dynamics of Telopea using the reference genome in conjunction with DArTseq (n = 244) and whole genome shotgun sequencing (n = 14) of each of the seven lineages; there are three lineages of T. speciosissima – coastal, upland, and southern. Here, I will discuss the population structure and demographic history of the genus. We also examined phylogenomic relationships and developed a scalable method of rapidly generating species trees from short-read data to maximise the recovery of informative data from genomic datasets. The waratah reference genome represents an important new genomic resource in Proteaceae to accelerate our understanding of the origins and evolutionary dynamics of the Australian flora.</p>
</blockquote>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-71991380259018127712021-06-03T10:42:00.000+10:002021-06-08T19:53:51.745+10:00Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0AOu_7S45bgPoi2qUodsr9rT7AZyMoU9hjx9Oe0DbDODXPEAmDBkr6IaYPIG7MQFXU7T0FY7AbqZnAJj8rWIIPyvQNhsy3XVRXyuXPgeRw3YcWiDoaxsxS3LIlDVcI7p_ddAsvZs-9A/s313/waratah.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="" border="0" height="320" data-original-height="313" data-original-width="235" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0AOu_7S45bgPoi2qUodsr9rT7AZyMoU9hjx9Oe0DbDODXPEAmDBkr6IaYPIG7MQFXU7T0FY7AbqZnAJj8rWIIPyvQNhsy3XVRXyuXPgeRw3YcWiDoaxsxS3LIlDVcI7p_ddAsvZs-9A/s320/waratah.jpg"/></a>The latest genomics paper from the lab is <a href="https://doi.org/10.1101/2021.06.02.444084">now out on bioRvix</a>. This is the first paper from <a href="https://edwardslab.blogspot.com/2019/05/stephanie-chen-phd-student.html">Stephanie Chen</a>’s PhD project in collaboration with the <a href="https://www.rbgsyd.nsw.gov.au/">Royal Botanic Gardens and Domain Trust (RBGDT), Sydney</a>. In this paper, Stephanie reports on the chromosome-level assembly of the <a href="https://en.wikipedia.org/wiki/Waratah">New South Wales Waratah</a>, the <a href="https://www.anbg.gov.au/emblems/nsw.emblem.html">floral emblem of NSW</a>. This is the first of the <a href="http://edwardslab.blogspot.com/2018/12/what-are-we-sequencing-next-waratah.html">pilot reference genomes</a> to be released from the <a href="https://www.genomicsforaustralianplants.com/">Genomics for Australian Plants</a> initiative.</p>
<p>In addition to the genome itself, this paper describes a couple of genomics tools from the lab. <strong>DepthSizer</strong> (<a href="https://github.com/slimsuite/depthsizer">https://github.com/slimsuite/depthsizer</a>) uses BUSCO predictions to establish the single-copy read depth of sequencing data, from which the genome size can be estimated in a way that is hopefully quite robust to assembly quality. <strong>Diploidocus</strong> (<a href="https://github.com/slimsuite/diploidocus">https://github.com/slimsuite/diploidocus</a>) has been used for our previous Dog genome assemblies to help eliminate “haplotigs” (heterozygous regions of the genome that appear in the assembly twice), and low-quality sequences, in addition to flagging possible collapsed repeats or contaminants for further investigation. Here, the Diploidocus “tidy” pipeline is considerably extended for a much more nuanced classification and filtering of scaffolds, using a combination of read depths, homology, kmer analysis and BUSCO predictions.</p>
<hr>
<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiOVbGs0_87OVP4v2ZlL4Pp0EY0XxhicdXgHFrRF-r72bbPM4bR4I7pyDhU_hM56w-BLLBdIO3R1cZE8AKA92G8hJMelPPwcnnMfzRfi06UdeV8ChEa16Y7eGrtDB8MlDVqOWKiHf6vnws/s324/chen2021.biorxiv.qr.png" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="" border="0" height="160" data-original-height="324" data-original-width="248" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiOVbGs0_87OVP4v2ZlL4Pp0EY0XxhicdXgHFrRF-r72bbPM4bR4I7pyDhU_hM56w-BLLBdIO3R1cZE8AKA92G8hJMelPPwcnnMfzRfi06UdeV8ChEa16Y7eGrtDB8MlDVqOWKiHf6vnws/s320/chen2021.biorxiv.qr.png"/></a><b>Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JS, Sauquet H, Bourke G, Bragg JG & <U>Edwards RJ</U> (preprint):</b> Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C. <i>bioRxiv</i> 2021.06.02.444084; doi: <a href="https://doi.org/10.1101/2021.06.02.444084">10.1101/2021.06.02.444084</a>.<br />
[<a href="https://doi.org/10.1101/2021.06.02.444084">bioRxiv</a>]</p>
<h2 id="abstract">Abstract</h2>
<blockquote>
<p><b>Background:</b> <i>Telopea speciosissima</i>, the New South Wales waratah, is Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. <b>Findings:</b> Here, we report the first chromosome-level reference genome for <i>T. speciosissima</i>. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 91.2 % of Embryophyta BUSCOs complete. We introduce a new method in Diploidocus (<a href="https://github.com/slimsuite/diploidocus">https://github.com/slimsuite/diploidocus</a>) for classifying, curating and QC-filtering assembly scaffolds. We also present a new tool, DepthSizer (<a href="https://github.com/slimsuite/depthsizer">https://github.com/slimsuite/depthsizer</a>), for genome size estimation from the read depth of single copy orthologues and find that the assembly is 93.9 % of the estimated genome size. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. Our results indicate that the waratah genome is highly repetitive, with a repeat content of 62.3 %. <b>Conclusions:</b> The <i>T. speciosissima</i> genome (Tspe_v1) will accelerate waratah evolutionary genomics and facilitate marker assisted approaches for breeding. Broadly, it represents an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.</p>
</blockquote>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-91124340666341928222021-05-31T09:45:00.003+10:002021-05-31T10:02:04.086+10:00Gabriella Cozijnsen (Honours student)<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBHyVgbXyiatIxt5cK1OrL8QovAlhjHdGvKvT1HIFOUjDo-dpI229RYZPcx2rJ0koOr14mESrMV4E_hQL0aKsf098DcUFE055gok9sjmNaEEGB5_edva8c4WScPB8LYBA3opd_wxjhdOc/s320/Gabriella_Headshot.jpg"><img alt="" border="0" height="320" data-original-height="2573" data-original-width="1222" align="right" style="margin-left:10px; margin-bottom:10px" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBHyVgbXyiatIxt5cK1OrL8QovAlhjHdGvKvT1HIFOUjDo-dpI229RYZPcx2rJ0koOr14mESrMV4E_hQL0aKsf098DcUFE055gok9sjmNaEEGB5_edva8c4WScPB8LYBA3opd_wxjhdOc/s320/Gabriella_Headshot.jpg"/></a>Gabriella Cozijnsen completed a Bachelor of Science from UNSW in 2020, majoring in genetics and physics with minor in chemistry. She commenced her honours (Genetics) with the Edwards Lab in Term 2, 2021.</p>
<p>Gabby’s project is to resolve and characterise the sex chromosomes in our two snakes sequenced as part of the <a href="https://babsgenome.blogspot.com/">BABS Genome Project</a> and in collaboration with the <a href="https://ausargenomics.com/">The Australian Amphibian and Reptile Genomics Initiative (AusARG)</a> and <a href="https://www.babs.unsw.edu.au/paul-waters">A/Prof Paul Waters</a>.</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-48169094314982270822021-04-19T23:08:00.049+10:002021-05-11T23:45:32.565+10:00Intergenerational effects of manipulating DNA methylation in the early life of an iconic invader<div class="separator" style="clear: both;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxR2JwsSAk98vmbWJOBVM3czoqVIgl5YWRNJXXYaqakaINgNb6ADEFDdBtM47Ohu1eQjT8ytB8ga6Osua7RKzN2Gj90IBWh5413J80YkPfJWe8EngQtWYK24wh50gMCxaodb_oibC823I/s250/button-canetoad.jpg" style="display: block; padding: 1em 0; text-align: center; clear: right; float: right;"><img alt="" border="0" width="250" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxR2JwsSAk98vmbWJOBVM3czoqVIgl5YWRNJXXYaqakaINgNb6ADEFDdBtM47Ohu1eQjT8ytB8ga6Osua7RKzN2Gj90IBWh5413J80YkPfJWe8EngQtWYK24wh50gMCxaodb_oibC823I/s320/button-canetoad.jpg"/></a></div>
<p>Another <a href="http://edwardslab.blogspot.com/search/label/cane%20toad">cane toad</a> paper has hit the shelves! This is another paper from our ongoing collaboration with <a href="http://www.eerc.unsw.edu.au/lee-ann-rollins">Lee Ann Rollins</a> and her great team of invasion biologists and molecular ecologists. This paper once again uses our <a href="http://edwardslab.blogspot.com/2018/08/draft-genome-assembly-of-invasive-cane.html">draft cane toad genome</a>* and builds on the <a href="http://edwardslab.blogspot.com/2020/06/do-epigenetic-changes-drive.html">previous cane toad methylation analysis</a> by PhD student Roshmi Sarma to look at some really interesting intergenerational effects.
[*Genome update coming soon - watch this space!]</p>
<p>Could this be epigenetic inheritance? Maybe. But it could also be some kind of parental germline thing. Either way, it’s a fascinating result and further evidence to support the fact that whilst our genome may establish our genetic potential, it does not control our destiny.</p>
<p>And if you want to know what it takes to identify effects like this, check out the mind-boggling experiment design Figure! (PDF available on request!)</p>
<hr>
<p>This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’</p>
<p><b>Sarma RR, Crossland MR, Eyck HJF, <u>Edwards RJ</u>, DeVore JL, Cocomazzo M, Zhou J, Brown GP, Shine R & Rollins LA (2021):</b> Intergenerational effects of manipulating DNA methylation in the early life of an iconic invader. <i>Philosophical Transactions of the Royal Society B</i> <b>376:</b>20200125.
[<a href="https://royalsocietypublishing.org/doi/abs/10.1098/rstb.2020.0125">Phil Trans Roy Soc B</a>]
[<a href="https://www.ncbi.nlm.nih.gov/pubmed/33866803">PubMed</a>]</p>
<h2 id="abstract">Abstract</h2>
<blockquote>
<p>In response to novel environments, invasive populations often evolve rapidly. Standing genetic variation is an important predictor of evolutionary response but epigenetic variation may also play a role. Here, we use an iconic invader, the cane toad (<i>Rhinella marina</i>), to investigate how manipulating epigenetic status affects phenotypic traits. We collected wild toads from across Australia, bred them, and experimentally manipulated DNA methylation of the subsequent two generations (G1, G2) through exposure to the DNA methylation inhibitor zebularine and/or conspecific tadpole alarm cues. Direct exposure to alarm cues (an indicator of predation risk) increased the potency of G2 tadpole chemical cues, but this was accompanied by reductions in survival. Exposure to alarm cues during G1 also increased the potency of G2 tadpole cues, indicating intergenerational plasticity in this inducible defence. In addition, the negative effects of alarm cues on tadpole viability (i.e. the costs of producing the inducible defence) were minimized in the second generation. Exposure to zebularine during G1 induced similar intergenerational effects, suggesting a role for alteration in DNA methylation. Accordingly, we identified intergenerational shifts in DNA methylation at some loci in response to alarm cue exposure. Substantial demethylation occurred within the sodium channel epithelial 1 subunit gamma gene (SCNN1G) in alarm cue exposed individuals and their offspring. This gene is a key to the regulation of sodium in epithelial cells and may help to maintain the protective epidermal barrier. These data suggest that early life experiences of tadpoles induce intergenerational effects through epigenetic mechanisms, which enhance larval fitness.</p>
</blockquote>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-86771326325042060452021-04-08T09:33:00.088+10:002021-06-08T19:53:51.745+10:00Transcript- and annotation-guided genome assembly of the European starling<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRS8W0UhkQyTLUK2F2svZ8vzM523c3of1n3nI2b-qUbgp8POomLyBCzUKFr8Zf0z9WOWgIUH95_hTgbevLHX1nNceKslwMNfCsbZ0TWw8gKvaQJVBvdyKPmK0H1pinTtgGwoC5_wFXESM/s1280/Stuart2021.F7.large.jpg" style="display: block; padding: 1em 0; text-align: center; clear: right; float: right;"><img alt="" border="0" width="320" data-original-height="1115" data-original-width="1280" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgRS8W0UhkQyTLUK2F2svZ8vzM523c3of1n3nI2b-qUbgp8POomLyBCzUKFr8Zf0z9WOWgIUH95_hTgbevLHX1nNceKslwMNfCsbZ0TWw8gKvaQJVBvdyKPmK0H1pinTtgGwoC5_wFXESM/s320/Stuart2021.F7.large.jpg"/></a>Our starling genome paper is now available as a pre-print on <a href="https://doi.org/10.1101/2021.04.07.438753">bioRxiv</a>! This was some great work by PhD student, <a href="http://edwardslab.blogspot.com/2018/02/katarina-stuart-phd-student.html">Kat Stuart</a>. Kat assembled a new Australian starling genome, using a combination of linked reads, low coverage long reads, and long-read PacBio iso-seq transcriptomics data. A second Illumina assembly of a North American group is also presented. As we saw with our <a href="https://edwardslab.blogspot.com/2021/03/chromosome-length-genome-assembly-and.html">Basenji genome paper</a>, having two (or more) genomes from a species can be really useful for disentangling real difference from assembly artefacts. (No assembly is perfect!)</p>
<p>This paper is a great example of how a bit of TLC and imagination can get the most out of data produced with a limited budget. We were unable to get deep long-read sequencing this time, but instead show the additional power that long-read full-length transcriptome data can provide in assembling a genome - above and beyond the annotation.</p>
<p>This paper also officially describes a couple of genomics tools from the lab <strong><a href="http://edwardslab.blogspot.com/2019/07/gsa2019-buscomp-busco-compilation-and.html">BUSCOMP</a></strong> has been in the works for some time, and this paper updates previous results to BUSCO v5 analysis and confirms <a href="http://edwardslab.blogspot.com/search?q=buscomp#poster168:buscomp:buscocompilationandcomparisonforassessingcompletenessinmultiplegenomeassemblies">our previous snake results</a> using starling-derived test data. BUSCO is a powerful and popular tool that estimates genome completeness using gene prediction and curated models of single-copy protein orthologues. However, we demonstrate how results can be counterintuitive: adding/removing scaffolds can alter BUSCO predictions elsewhere in the assembly, while low sequence quality may reduce “completeness” scores and miss genes that are present in the assembly. BUSCOMP (BUSCO Compilation and Comparison) (<a href="https://github.com/slimsuite/buscomp">https://github.com/slimsuite/buscomp</a>) complements BUSCO to identify/overcome these issues by compiling a non-redundant set of the highest-scoring single-copy BUSCO complete sequences and re-searching these against assemblies for consistent completness scoring. <strong>SAAGA</strong> (<a href="https://github.com/slimsuite/saaga">https://github.com/slimsuite/saaga</a>) is a new tool for annotation versus reference proteome comparisons. SAAGA can compare different annotations of the same assembly, or be combined with a lightweight annotation tool like GeMoMa to compare different assemblies of the same organism.</p>
<hr>
<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjXYO47JQdpTCENZnZP2rbZFjQKhaHnSi7PM7aybT17iMD6hyphenhyphen3dhpFCgODESJWVF8WRKCGCkQXg8jL3hzOCYP6kNXyPAPZkrYS77HNiAsPn5qBSlaO9djlyz7vJH-7D0FRP_OvSTFhUt1Q/s324/Stuart2021.biorxiv.qr.png" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="" border="0" height="160" data-original-height="324" data-original-width="248" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjXYO47JQdpTCENZnZP2rbZFjQKhaHnSi7PM7aybT17iMD6hyphenhyphen3dhpFCgODESJWVF8WRKCGCkQXg8jL3hzOCYP6kNXyPAPZkrYS77HNiAsPn5qBSlaO9djlyz7vJH-7D0FRP_OvSTFhUt1Q/s320/Stuart2021.biorxiv.qr.png"/></a><b>Stuart KC<em>, <U>Edwards RJ</U></em>, Cheng Y, Warren WC, Burt DW, Sherwin WB, Hofmeister NR, Werner SJ, Ball GF, Bateson M, Brandley MC, Buchanan KL, Cassey P, Clayton DF, De Meyer T, Meddle SL & Rollins LA (preprint):</b> Transcript- and annotation-guided genome assembly of the European starling. <i>bioRxiv</i> 2021.04.07.438753; doi: <a href="https://doi.org/10.1101/2021.04.07.438753">10.1101/2021.04.07.438753</a>. [*Joint first authors]
[<a href="https://www.biorxiv.org/content/10.1101/2021.04.07.438753v1">bioRxiv</a>]</p>
<h2 id="abstract">Abstract</h2>
<blockquote>
<p>The European starling, <i>Sturnus vulgaris</i>, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (<i>S. vulgaris</i> vAU), and a second North American genome (<i>S. vulgaris</i> vNA), as complementary reference genomes for population genetic and evolutionary characterisation. <i>S. vulgaris</i> vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 1,628 scaffolds (72.5 Mb scaffold N50). Species-specific transcript mapping and gene annotation revealed high structural and functional completeness (94.6% BUSCO completeness). Further scaffolding against the high-quality zebra finch (<i>Taeniopygia guttata</i>) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Rapid, recent advances in sequencing technologies and bioinformatics software have highlighted the need for evidence-based assessment of assembly decisions on a case-by-case basis. Using <i>S. vulgaris</i> vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, SAAGA) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counter-intuitive behaviour in traditional BUSCO metrics, and present BUSCOMP, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. Finally, we present a second starling assembly, <i>S. vulgaris</i> vNA, to facilitate comparative analysis and global genomic research on this ecologically important species.</p>
</blockquote>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-23080205017049960182021-03-18T13:58:00.000+11:002021-06-08T19:53:51.744+10:00Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome<p>Our latest genome paper <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiWkxsAKnSmcMjUCgXDCl7F50Ovhi0ouQnBy4oJRS_nh8_8TT-qnjo3qQ4X0BLlNL9FjBrNhWgD6JWAqc9Sj-p77rkXlq2q_y_ctVNcAADqVtAzvJmcFIbrFd5hC-M8G06OpnYSmLX9a0M/s2048/China.jpg" ><img alt="" border="0" width="300" style="margin-left:10px;" align="right" data-original-height="1687" data-original-width="2048" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiWkxsAKnSmcMjUCgXDCl7F50Ovhi0ouQnBy4oJRS_nh8_8TT-qnjo3qQ4X0BLlNL9FjBrNhWgD6JWAqc9Sj-p77rkXlq2q_y_ctVNcAADqVtAzvJmcFIbrFd5hC-M8G06OpnYSmLX9a0M/s300/China.jpg"/></a>
is now out at <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07493-6">BMC Genomics</a>. This was a second collaboration in the team behind the <a href="http://edwardslab.blogspot.com/2020/04/canfamgsd-de-novo-chromosome-length.html">German Shepherd Dog genome</a> last year, led by Bill Ballard. This time, we used a combination of BGI short reads, ONT long reads, and Hi-C scaffolding to generate a chromosome-length assembly. This is one of the most intact and complete dog genomes generated to date, and joins only a handful of published breed-specific chromosome-length assemblies.</p>
<p>The Basenji is particularly interesting as it sits at the base of the dog breed family tree, making it a good unbiased reference for future comparisons between breeds.</p>
<p>The paper also has a few nice nuggets for those interesting in genome assembly. Of particular interest, our initial assembly had an artefact where the entire mitochondrial genome got assembled (in two copies) into the middle of one of the nuclear chromosomes. It is not entirely clear why this happened, but it was inserted into a <a href="https://en.wikipedia.org/wiki/NUMT">NUMT</a> (nuclear mitochondrial DNA insertion) fragment at that location. To make finding such things easier, we’ve released a new NUMT finding tool, <a href="https://github.com/slimsuite/numtfinder">NUMTFinder</a>.</p>
<p>As with our previous dog genome, the <a href="http://edwardslab.blogspot.com/2020/04/canfamgsd-de-novo-chromosome-length.html">German Shepherd Dog</a>, we also observe that the tandem repeat of <em>Amy2B</em> (Amylase Alpha 2B) genes, was assembled intact but with fewer copies than are present in the actual genome. (This gene is of interest for <a href="https://pubmed.ncbi.nlm.nih.gov/23354050/">dog domestication and adaptations to a starch-rich diet</a>.) Crucially, without looking at the raw sequencing data, it would not have been clear that the assembly under-represents <em>Amy2B</em> copy number. This kind of analysis can be repeated using the <code>regcheck</code> or <code>regcnv</code> run modes of <a href="https://github.com/slimsuite/diploidocus">Diploidocus</a>, which estimates the copy number of a region based on its read depth versus the single-copy read depth determined from <a href="https://busco.ezlab.org/">BUSCO</a> single-copy complete genes.</p>
<p>Overall, this presents a nice case study of the need for a bit of TLC and manual curation, even when you have some very impressive completeness and contiguity statistics.</p>
<hr />
<p><b><u>Edwards RJ</u>, Field MA, Ferguson JM, Dudchenko O, Keilwagen K, Rosen BD, Johnson GS, Rice ES, Hillier L, Hammond JM, Towarnicki SG, Omer A, Khan R, Skvortsova K, Bogdanovic O, Zammit RA, Lieberman Aiden E, Warren WC & Ballard JWO (2021):</b> Chromosome-length genome assembly and structural variations of the primal Basenji dog (<i>Canis lupus familiaris</i>) genome. <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07493-6"><i>BMC Genomics</i> <b>22:</b>188</a></p>
<h2 id="abstract">Abstract</h2>
<blockquote>
<p><b>Background:</b> Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness.</p>
<p><b>Results:</b> Here, we report two high quality <i>de novo</i> Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection.</p>
<p><b>Conclusions:</b> The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.</p>
</blockquote>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0tag:blogger.com,1999:blog-31511029258923306.post-81968611958711679012021-02-15T09:46:00.001+11:002021-05-31T09:52:10.113+10:00Cadel Watson (Honours student)<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvEQ2DDDBK_vz_kU-6E2xVb_SOJc6eR916mBAwxkJENnW2tJDVdJ3_L6La3defyk2zro90ur3bavFC7JtbYiVVW-kEZj2UCARKRC0fCxfnYY-CvjX4-k6yhT0OsF9CfoMwh6nJH3XL54k/s390/Cadel+Watson+-+Headshot.png"><img alt="" border="0" width="320" data-original-height="368" data-original-width="390" align="right" style="margin-left:10px; margin-bottom:10px" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvEQ2DDDBK_vz_kU-6E2xVb_SOJc6eR916mBAwxkJENnW2tJDVdJ3_L6La3defyk2zro90ur3bavFC7JtbYiVVW-kEZj2UCARKRC0fCxfnYY-CvjX4-k6yhT0OsF9CfoMwh6nJH3XL54k/s320/Cadel+Watson+-+Headshot.png"/></a>Cadel Watson joined the lab in 2021 as an Honours student. His project focuses on the identification of ultra-conserved elements in genomes, including exploring their definition and building analysis tools, and potential applications of UCEs to assessing genome completeness. Cadel is in the final year of a Bachelor of Engineering (Bioinformatics) degree.</p>
<p>[<a href="https://www.linkedin.com/in/cadel-watson-bb7b2414b/">LinkedIn</a>]</p>Richard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.com0