A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes

Chen SH, Martino AM, Luo Z, Schwessinger B, Jones A, Tolessa T, Bragg JG, Tobias PA, Edwards RJ (2023): A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes. GigaScience 12:giad102. [Gigascience] [PubMed]

Background. Melaleuca quinquenervia (broad-leaved paperbark) is a coastal wetland tree species that serves as a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. While extensively cultivated for its ornamental value, it has also become invasive in regions like Florida, USA. Long-lived trees face diverse pest and pathogen pressures, and plant stress responses rely on immune receptors encoded by the nucleotide-binding leucine-rich repeat (NLR) gene family. However, the comprehensive annotation of NLR encoding genes has been challenging due to their clustering arrangement on chromosomes and highly repetitive domain structure; expansion of the NLR gene family is driven largely by tandem duplication. Additionally, the allelic diversity of the NLR gene family remains largely unexplored in outcrossing tree species, as many genomes are presented in their haploid, collapsed state.

Results. We assembled a chromosome-level pseudo-phased genome for M. quinquenervia and described the allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, distinct clustering patterns, and differences in the types and numbers of novel integrated domains.

Conclusions. The high-quality M. quinquenervia genome assembly establishes a new framework for functional and evolutionary studies of this significant tree species. Our findings suggest that maintaining allelic diversity within the NLR gene family is crucial for enabling responses to environmental stress, particularly in long-lived plants.

PAG Australia 2023: Exploring Dingo Ecology and Evolution with Chromosome-Level Canid Genomes

Richard J Edwards, Matt F Field and J William O Ballard - PAG Australia 2023

Dogs are uniquely associated with human dispersal and bring novel insight into human migration and the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. The exact origin(s) and people(s) who transported the canines that became dingoes to Australia is debated, but it has been suggested they arrived by boat ~5,000-8,000 BP. Published morphological and genetic evidence has established the presence of at least two dingo lineages. The Alpine dingo is commonly found in south-eastern Australia while the Desert ecotype is found in the north, central and western Australia. The relationship of dingoes to modern dogs, and the ecotypes to each other, has important implications management and protection of this top predator, as well as providing interesting perspectives on human colonisation and canine domestication.

We have generated chromosome-level assemblies of both dingo ecotypes, along with domesticated dogs representing both ancient (Basenji) and derived (German Shepherd) breeds. In each case, long-read sequencing and Hi-C scaffolding have been combined to produce genome assemblies with high contiguity and structural completeness. Comparison of these assemblies with additional dog breeds, using the Greenland wolf as an outgroup, places the dingo as an early offshoot of modern dogs, situated between the grey wolf and the domesticated dogs of today. This is supported by patterns of genetic variation, and chromosome structure. Furthermore, we confirm that dingoes have not experienced the expansion of the AMY2B pancreatic amylase gene that occurred during domestication of modern dogs. This has important implications for dingo ecology and behaviour, and raises the prospect of using AMY2B copy number as a novel and reliable in-field discriminator between dingoes and feral dogs.

The OceanOmics Centre is hiring! Research technician positions available

We are recruiting two new positions for the Minderoo OceanOmics Centre at UWA: a Marine Genomics Research Technician and an eDNA Research Technician / Scientific Officer. These are both full-time two-year positions (with likely opportunities for extension), and applications close 11:55 PM AWST on Sunday, 6 August 2023. Please see the link below to find out more. Informal enquiries are also welcome - please contact Rich Edwards.

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.

About the team

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.

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.

For more details, and to apply, visit the UWA jobs site: https://external.jobs.uwa.edu.au/cw/en/job/512661 and https://external.jobs.uwa.edu.au/cw/en/job/514981.

We are also recruiting students for three Pawsey student internships.

Three Pawsey Internship projects available for the Ocean Genomes Project

We have three Pawsey student internships available this summer with the Ocean Genomes Laboratory in the Minderoo OceanOmics Centre at UWA. Closing date: 07 August, 2023 at 17:00 AWST (Perth time). This is a 10-week, paid program open to exceptional undergrad (2nd/3rd year), Honours, Master’s and PhD students. Apply at the CSIRO Application page. Please get in touch if you want to know more and/or are interested in a student research project in the lab.

Optimising workflows for whole genome assembly for marine vertebrates (Project #04)

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.

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.

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.

A containerised Pawsey workflow for Diploidocus (Project #10)

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 Diploidocus 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.

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.

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.

A containerised Pawsey workflow high throughput phylogenomics (Project #14)

This project aims to produce a robust and efficient phylogenomics workflow for whole genome sequencing data.

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 BUSCOMP; (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.

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.

This project will adapt the wgs2tree 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.

The Minderoo OceanOmics Centre at UWA is hiring - lab manager position available

We are recruiting a new lab manager position for the Minderoo OceanOmics Centre at UWA. This is a full-time three-year position, available at Level 6 or 7, depending on experience. Applications close 11:55 PM AWST on Thursday, 13 July 2023. Please see the link below to find out more. Informal enquiries are also welcome - please contact Rich Edwards.

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.

About the team

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.

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.

For more details, and to apply, visit the UWA jobs site: https://external.jobs.uwa.edu.au/cw/en/job/514000.

Watch this space for some further opportunities coming soon: two laboratory research technicians, and three Pawsey student internships.

The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology

Ballard JWO, Field MA, Edwards RJ, Wilson LAB, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V & Aiden EL (2023): The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology. Gigascience 12:giad018. [Gigascience] [PubMed]

Background

One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed.

Findings

We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog.

Conclusions

These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.

Contrasting Patterns of Single Nucleotide Polymorphisms and Structural Variation Across Multiple Invasions

Stuart KC, Edwards RJ, Sherwin WB & Rollins LA (2023): Contrasting patterns of single nucleotide polymorphisms and structural variations across multiple invasions. Mol. Biol. Evol. 40:msad046. [Mol. Biol. Evol.] [PubMed] [bioRxiv]

Genetic divergence is the fundamental process that drives evolution and ultimately speciation. Structural variants (SVs) are large-scale genomic differences within a species or population and can cause functionally important phenotypic differences. Characterizing SVs across invasive species will fill knowledge gaps regarding how patterns of genetic diversity and genetic architecture shape rapid adaptation under new selection regimes. Here, we seek to understand patterns in genetic diversity within the globally invasive European starling, Sturnus vulgaris. Using whole genome sequencing of eight native United Kingdom (UK), eight invasive North America (NA), and 33 invasive Australian (AU) starlings, we examine patterns in genome-wide SNPs and SVs between populations and within Australia. Our findings detail the landscape of standing genetic variation across recently diverged continental populations of this invasive avian. We demonstrate that patterns of genetic diversity estimated from SVs do not necessarily reflect relative patterns from SNP data, either when considering patterns of diversity along the length of the organism’s chromosomes (owing to enrichment of SVs in subtelomeric repeat regions), or interpopulation diversity patterns (possibly a result of altered selection regimes or introduction history). Finally, we find that levels of balancing selection within the native range differ across SNP and SV of different classes and outlier classifications. Overall, our results demonstrate that the processes that shape allelic diversity within populations is complex and support the need for further investigation of SVs across a range of taxa to better understand correlations between often well-studied SNP diversity and that of SVs.

Happy New Year, starling lovers!

Stuart KC, Sherwin WB, Edwards RJ & Rollins LA (2023): Evolutionary genomics: Insights from the invasive European starlings. Frontier in Genetics 13:1010456. [Front Genet] [PubMed]

Two fundamental questions for evolutionary studies are the speed at which evolution occurs, and the way that this evolution may present itself within an organism’s genome. Evolutionary studies on invasive populations are poised to tackle some of these pressing questions, including understanding the mechanisms behind rapid adaptation, and how it facilitates population persistence within a novel environment. Investigation of these questions are assisted through recent developments in experimental, sequencing, and analytical protocols; in particular, the growing accessibility of next generation sequencing has enabled a broader range of taxa to be characterised. In this perspective, we discuss recent genetic findings within the invasive European starlings in Australia, and outline some critical next steps within this research system. Further, we use discoveries within this study system to guide discussion of pressing future research directions more generally within the fields of population and evolutionary genetics, including the use of historic specimens, phenotypic data, non-SNP genetic variants (e.g., structural variants), and pan-genomes. In particular, we emphasise the need for exploratory genomics studies across a range of invasive taxa so we can begin understanding broad mechanisms that underpin rapid adaptation in these systems. Understanding how genetic diversity arises and is maintained in a population, and how this contributes to adaptability, requires a deep understanding of how evolution functions at the molecular level, and is of fundamental importance for the future studies and preservation of biodiversity across the globe.