Monday 11 October 2021

SLiMSuite Short Linear Motif and Genomics Analysis Tools: BUSCOMP v0.13.0 (MetaEuk) release

SLiMSuite: BUSCOMP v0.13.0 (MetaEuk) release: BUSCOMP v0.13.0 is now on GitHub. 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 *.fna files where possible.

Congratulations to the Edwards Lab #GSAA21 Award winners

Congratulations to Katarina Stuart, Stephanie Chen, and Cadel Watson, who all won prizes at this year’s Genetics Society of AustralAsia 2021 Conference.

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!

Wednesday 6 October 2021

Edwards Lab at Genetics Society of AustralAsia 2021 #GSAA21

Look out for some interesting genomics talks by Edwards Lab members at this year’s Genetics Society of AustralAsia 2021 conference, which started today. Congratulation to Stephanie for winning the Spencer Smith-White Travel Award (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.

Thursday 7th October: Genomics and Transcriptomics Session | 1:30-2:00 (Lightning talks)

Cadel Watson - dedUCE: efficient identification of Ultraconserved Elements from multiple genomes

Cadel Watson, Mitchell J. Cummins, Yasir Kusay, Maxine Halbheer, Eric Urng, John S. Mattick and Richard J. Edwards

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.

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.

  1. 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.

  2. 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.

Friday 8th October: Ecological and Evolutionary Genetics Session | 10:45-11:00

Katarina Stuart - A genetic perspective on rapid adaptation in the globally invasive European starling (Sturnus vulgaris)

Stuart KC, Sherwin WB, Edwards RJ & Rollins LA

Few invasive birds are as globally successful or as well-studied as the common starling (Sturnus vulgaris). 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.

Friday 8th October: Spencer Smith-White Travel Award recipient | 1:15-1:30

Stephanie Chen - Genomics of speciation and introgression: insights from waratah (Telopea spp.) as a model clade

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 T. speciosissima (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.