BioDiversity Genomics Conference (BG24)

The global BioDiversity Genomics Conference (BG24) was another great success this year. As well as running a session on Marine Vertebrate Genomics, it was particularly rewarding to see some many quality contributions from lab members and alumni.

Biodiversity Genomics in Australasia

Jessica Pearce (UWA): Reconstructing tiger shark history using genomics

Sharks and rays are a clade of high evolutionary, ecological, economic, and cultural significance, and yet they are one of the most threatened taxa groups in the marine environment. Despite this, there remains a lack of molecular resources for this class to assist with their conservation. The tiger shark (Galeocerdo cuvier) is a near threatened, keystone species distributed circumglobally that is under substantial pressure from human impacts, making it a high priority for management worldwide. We sequenced and characterised a reference quality assembly for the tiger shark, the first genome for this family, and used this to dive deeper into the evolution, adaption, and demographic history of this ancient species. We investigated how its effective population size (Ne), genome-wide heterozygosity and inbreeding has changed over time to infer how this species has responded to past global events, and hence potential responses to ongoing and future accumulating threats. This aims to assist in effective management of this high-profile species. 

Katarina Stuart (University of Auckland): Lifetime fitness is correlated more strongly with structural variant than SNP mutational load in a threatened bird species

Conservation genomics is becoming increasingly interested in whether structural variant (SV) information can help the management of threatened species. The functional consequences of SVs are more complex than for single nucleotide polymorphisms (SNPs) and thus may be more likely to contribute to load. While the impacts of SV-specific genetic load may be less consequential for large populations, the interplay between weakened selection and stochastic processes mean that smaller populations, like those of the threatened Aotearoa hihi/New Zealand stitchbird (Notiomystis cincta), may harbour a high SV load. Hihi were once confined to a single remnant population, but have been reestablished into six sanctuaries and reserves, often via secondary bottlenecks, resulting in low genetic diversity, low adaptive potential and inbreeding depression. In this study, we use whole genome resequencing of 30 individuals from the Tiritiri Matangi population to identify the nature and distribution of both SNPs and SVs within this small avian population. We find that SNP and SV individual mutation load is only moderately correlated, likely because SVs arise in regions of high recombination and reduced evolutionary conservation. Finally, we leverage a long-term monitoring dataset of pedigree and fitness data to assess the impact of SNP and SV mutation load on individual fitness, and demonstrate that SV load correlates more strongly than SNP load with lifetime fitness. The results of this study indicate that only examining SNPs neglects important aspects of intraspecific variation, and that studying SVs has direct implications for linking genetic diversity and genetic health to inform management decisions.

Richard Edwards (UWA): Improving Hifiasm assemblies with 20 kb ONT reads

The quality and quantity of genome assembly has improved dramatically over recent years. Many large-scale genome projects assemble HiFi and HiC reads using Hifiasm to produce contiguous phased assemblies, scaffolded to chromosome-level. Nevertheless, HiFi reads are typically under 25 kb and can still struggle to assemble long, low-diversity repeat regions. Obtaining ‘ultra-long’ (100 kb or longer) ONT reads to solve this problem remains a significant challenge due to technical constraints and DNA sample requirements. Here, we explore the utility of using standard ONT long reads (20 kb or more) as ‘ultra-long’ input to improve phased Hifiasm assemblies for 22 species of bony fish (Genome Size, 627 Mb - 1.54 Gb). We also explore whether the new ‘telo-m’ mode in Hifiasm v0.9.0 improves telomere prediction in these species. Incorporating 20+ kb ONT reads (7.8X - 93.5X) significantly increased assembly contiguity. BUSCO completeness was not significantly altered, although there was some re-partitioning of BUSCO genes between phased haplotypes for some species. Improvement did not strongly correlate with read depth (neither HiFi nor ONT), suggesting that the underlying read length distributions and/or specific genome features are more important for determining the outcome. Hifiasm ‘telo-m’ mode significantly increased telomere recovery, assembling over six times the number of gapless telomere-to-telomere chromosomes when combined with incorporation of ONT reads. Verification of how these results translate to the quality and/or ease of curation of final HiC-scaffolded chromosome-level assemblies is ongoing, with a goal to determine whether the additional sample preparation and sequencing in the lab is cost-effective.

Emma de Jong (UWA): High-Quality Genomes for Australian Lutjanidae Species

Lutjanidae (snappers) are highly valued in commercial and recreational fisheries worldwide and some species serve as fisheries indicator species particularly for bioregions in Western Australia. Comprehensive genomic mapping of immune gene families of Lutjanidae species are lacking, but this information can inform understanding disease vulnerability, the impact of environmental stress, improving aquaculture efforts and to provide insights into the health of wild populations. Despite their importance, only 3 out of 113 Lutjanid species currently have available reference genomes, two of which are highly fragmented (>11,000 and >200,000 contigs), impacting studies on gene families relevant to aquaculture. In this study, we present high-quality chromosome-level reference genomes for 14 Australian lutjanid species across seven genera, generated using PacBio HiFi and Dovetail HiC data. We present initial comparative genomic analyses, including immune gene content and chromosomal synteny analyses across species. These analyses provide insights into the genomic architecture and evolutionary relationships within Lutjanidae. Ongoing work aims to comprehensively map and compare the immune gene family repertoire across genera in Lutjanidae, as well as lethrinid species as an outgroup, to determine genus-specific changes in genes (e.g., loss, selection, duplication) important for pathogen detection, antigen presentation, inflammation, and immune memory. These genome assemblies will serve as a foundational resource to the wider scientific community interested in these species.

Research of ECRs who work in biodiversity genomics

Lara Parata (UWA): Genome Evolution in Marine Ray-Finned Fishes

Approximately half of extant vertebrate species are fishes, with more than 30,000 species classified as ray-finned fishes (Actinopterygii). Actinopterygii represent diverse phenotypes, feeding strategies, life history traits and occupy distinct ecological niches, making them an ideal taxa for studying molecular drivers of diversity and adaptation. Despite their diversity, ecological, and economical importance, only 145 Illumina genome assemblies are available for marine Actinopterygii species. In this study we present 250 new marine Actinopterygii genome assemblies generated using Illumina whole genome sequencing and initial results from a large-scale study of these 395 genomes. Using reference-based annotation tools we determine which fish families have unique patterns of gene family frequency / structure (e.g., losses, expansions, contractions), and correlate these with predicted functional signatures to infer biological and ecological adaptations. We identify fish families with distinct rates of change in the gene families present within their genomes (e.g., more losses / expansions or diversity) and associate these patterns with increased rates of diversification or speciation to further elucidate the genomic attributes contributing to ecological success. The results of this work contribute to the growing understanding of fish genome evolution and provide new insights into the evolutionary history and ecological success of marine Actinopterygii.