Biology subjects

O'Toole, B.

Publications and source records attributed to O'Toole, B..

4 recordsLinked to original sources

bioRxiv2025

Chromosome-level genome assembly of the Brazilian merganser (Mergus octosetaceus), a rare and elusive waterfowl species

BackgroundThe Brazilian merganser (Mergus octosetaceus) is a critically endangered bird, with fewer than 250 mature individuals remaining in fragmented populations of the Cerrado biome in Brazil. It is an ecologically demanding species that requires clear water of fast-flowing rivers for diving and foraging, and riverside cavities for nesting. Technical and logistical challenges have restricted sampling and research to few genetic studies so far. The genetic results consistently revealed a low genetic diversity and high inbreeding in the species. Besides, the lack of a reference genome has precluded deeper evolutionary and conservation genetic analyses for the species. ResultsWe generated the first high-quality, chromosome-level genome assembly for Mergus octosetaceus using PacBio HiFi long reads and Arima Hi-C data from a female specimen. The assembly is 1.25 Gb in length, is highly complete, scoring 98.9% of BUSCO completeness, and includes both sex chromosomes (Z and W). Annotated repetitive elements comprise 18.94% of the genome, with evidence of recent activity, particularly among LINEs and LTRs retrotransposons. We also produced and annotated the complete mitochondrial genome, identifying 37 genes and the control region. Comparative synteny analysis with other Anatidae species revealed strong chromosomal conservation, with several inversion events in macrochromosomes. Demographic history reconstruction indicated fluctuations in effective population size, with significant reductions overlapped by major temperature changes, highlighting potential climate sensitivity of this lineage. ConclusionThis reference genome provides a fundamental resource for M. octosetaceus, enabling insights into genome evolution, chromosomal dynamics within Anatidae, and past population history. It is a remarkable foundation for future research and conservation strategies for managing and restoring this critically endangered species.

evolutionary biology↗

bioRxiv2025

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

BackgroundReference genomes for the entire sea turtle clade have the potential to reveal the genetic basis of traits driving the ecological and phenotypic diversity in these ancient and iconic marine species. Furthermore, these genomic resources can support conservation efforts and deepen our understanding of their unique evolution. ResultsWe present haplotype-resolved, chromosome-level reference genomes and high-quality gene annotations for five sea turtle species. This completes the catalog of reference genomes of the entire sea turtle clade when combined with our previously published reference genomes. Our analysis reveals remarkable genome synteny and collinearity across all species, despite the clades origin dating back more than 60 million years. Regions of high interspecific genetic distance and intraspecific genetic diversity are consistently clustered in genomic hotspots, which are enriched with genes coding for immune response proteins, olfactory receptors, zinc fingers, and G-protein-coupled receptors. These hotspot regions may offer insights into the genetic mechanisms driving phenotypic divergence among species, and represent areas of significant adaptive potential. Ancient demographic analysis revealed a synchronous population expansion among sea turtle species during the Pleistocene, with varying magnitudes of demographic change, likely shaped by their diverse ecological adaptations, and biogeographic contexts. ConclusionsOur work provides genomic resources for exploring genetic diversity, evolutionary adaptations, and demographic histories of sea turtles. We outline genomic regions with increased diversity, linked to immune response, sensory evolution, and adaptation to varying environments that have historically been subject to strong diversifying selection, and likely will underpin sea turtles responses to future environmental change. These reference genomes can assist conservation by providing insights into the demographic and evolutionary processes that sustain and threaten these iconic species.

genomics↗

bioRxiv2025

Insights into the Evolution of Ancient Shark and Ray Sex Chromosomes

While sex-determining mechanisms have been extensively characterized in many vertebrates, they have not been explored in chondrichthyan fishes until relatively recently. In the present study, we used high-quality whole genome reference assemblies to examine the putative sex chromosomes of 14 elasmobranch species spanning nine orders. We describe four newly assembled reference genomes belonging to the white shark Carcharodon carcharias, the Atlantic stingray Hypanus sabinus, the smalltooth sawfish Pristis pectinata, and the zebra shark Stegostoma tigrinum. We conducted sex chromosome identification and verification using short-read sequence data collected for multiple individuals for three of the species. This revealed putative pseudoautosomal regions (PARs) and, in one instance, a candidate sex chromosome reassignment. A synteny analysis revealed an ancient and shared origin of the chromosomes within elasmobranchs considerably older than any previously proposed scenario, and a potential candidate gene involved in sex determination shared across all examined species. The synteny analysis also revealed a historical fusion and the formation of neo-Y chromosomes between two myliobatiform species. Our results show that there has been strong conservation and homology of the X chromosomes among elasmobranchs in spite of their varied features and different evolutionary histories.

evolutionary biology↗

bioRxiv2023

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last [~]500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).

bioinformatics↗