Wednesday, 23 November 2022

Minderoo OceanOmics Centre at UWA Grand Opening

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: https://lnkd.in/gCP4GAhs

You can find out a bit more about the Minderoo OceanOmics Centre at UWA here: https://lnkd.in/gmXKjXNu

And the broader Minderoo OceanOmics program here: https://lnkd.in/gtKHSk7g

Or get in touch if you want to know more!

Friday, 21 October 2022

The Ocean Genomes Lab is hiring - Bioinformatics and Sequencing technicians wanted!

Adding to the recently advertised Sequencing technician posts (closing 27 October), we are now pleased to advertise two bioinformatics research assistant positions 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!

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).

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.

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.

The closing date for applications is 11:55 PM AWST on Thursday 10 November 2022.

To learn more about these opportunities, please click here or contact Rich Edwards at rich.edwards@uwa.edu.au.

ABOUT THE TEAM

The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and Computational Biology Services.

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.

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.

Thursday, 6 October 2022

The Ocean Genomes Laboratory is hiring!

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 Sequencing Specialist Scientific Officer, and two Sequencing Technician 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).

The closing date for applications is 11:55 PM AWST on Thursday 27 October 2022.

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.

About the team

The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and Computational Biology Services.

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.

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.

Monday, 8 August 2022

Senior Postdoc wanted for UWA Ocean Genomes Lab! (Closing soon)

The new Ocean Genomes Laboratory (part of the Minderoo OceanOmics Centre at the UWA Oceans Institute) is hiring a Level B postdoc in marine genomics. (Three-year fixed term full time role, or flexible working equivalent.)

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 Vertebrate Genome Project. You will also have an important role in helping to supervise the lab staff and research team.

Closing date: 11:55pm AWST, Friday 12 August 2022

Please see the UWA job advert for more details.

About the team

The Minderoo OceanOmics Centre at UWA combines a joint Ocean Genomes Laboratory, an OceanOmics Laboratory, and a Computational Biology Program.

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.

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.

About the opportunity

As a Research Fellow you will join a research group committed to applying modern molecular biological methods to marine research.

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.

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.

Friday, 22 July 2022

The Edwards Lab is moving to the UWA Oceans Institute!

More details will follow but, in August, I will be starting a new position at the University of Western Australia Oceans Institute to head up the new Ocean Genomes Laboratory as part of the Minderoo OceanOmics Centre. This exciting project will collaborate closely with the Minderoo Foundation, the Vertebrate Genome Project, and scientists across Australia to create marine vertebrate reference genomes.

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: http://bit.ly/OceanOmics. 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.

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!

Wednesday, 29 June 2022

The starling genome is out!

See the pre-print post for details.

Stuart KC*, Edwards RJ*, 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 (2022): Transcript- and annotation-guided genome assembly of the European starling. Molecular Ecology 22(8):3141-3160. doi: 10.1111/1755-0998.13679. [*Joint first authors] [Mol Ecol Res] [PubMed] [bioRxiv]

The European starling, Sturnus vulgaris, 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 (S. vulgaris vAU), and a second, North American, short-read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Species-specific transcript mapping and gene annotation revealed good gene-level assembly and high functional completeness. Using S. vulgaris 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 counterintuitive 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. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.

Saturday, 23 April 2022

The Australian dingo is an early offshoot of modern breed dogs

Field MA, Yadav S, Dudchenko O, Esvaran M, Rosen BD, Skvortsova K, Edwards RJ, Keilwagen J, Cochran BJ, Manandhar B, Bustamante S, Rasmussen JA, Melvin RG, Chernoffl B, Omer A, Colaric Z, Chan EKF, Minoche AE, Smith TPL, Gilbert MTP, Bogdanovic O, Zammit RA, Thomas T, Aiden EL & Ballard JWO (2022): The Australian dingo is an early offshoot of modern breed dogs. Science Advances 8(16):abm5944; DOI: 10.1126/sciadv.abm5944. [Sci Adv] [PubMed] [PDF]

Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.