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.

Evolutionary genomics: Insights from the invasive European starlings

Happy New Year, starling lovers! Our latest paper, looking at evolutionary insights gleaned from the starling genome during Kat Stuart's PhD, is now out in Frontiers in Genetics:

Stuart KC, Sherwin WB, Edwards RJ & Rollins LA (2023): Evolutionary genomics: Insights from the invasive European starlings. Frontiers 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.

Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ‘Candidatus Formimonas warabiya’ strain DCMF

Holland SI, Vázquez-Campos X, Ertan H, Edwards RJ, Manefield MJ & Lee M (2022): Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ' Candidatus Formimonas warabiya' strain DCMF. Front Microbiol. 13:1035247. doi: 10.3389/fmicb.2022.1035247 [Front Microbiol.] [PubMed]

Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood–Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, ‘Candidatus Formimonas warabiya’ strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.

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!

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.

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.