A comparative genomics multitool for scientific discovery and conservation

Abstract

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

Highly contiguous assemblies of 101 drosophilid genomes

“…Currently, a number of large consortia are leading well-publicized efforts to assemble the genomes of many taxa throughout the Tree of Life. Some often overlapping examples include the Vertebrate Genomes Project (Rhie et al, 2021), the Bird 10,000 Genomes Project , the Zoonomia Project (Genereux et al, 2020), the Darwin Tree of Life (Threlfall & Blaxter, 2021), the Earth Biogenome Project (Lewin et al, 2018), and the 5000 Arthropod…”

“…Currently, a number of large consortia are leading well-publicized efforts to assemble the genomes of many taxa throughout the Tree of Life. Some often overlapping examples include the Vertebrate Genomes Project ( Rhie et al, 2021 ), the Bird 10,000 Genomes Project ( Feng et al, 2020 ), the Zoonomia Project ( Zoonomia Consortium et al, 2020 ), the Darwin Tree of Life ( Threlfall and Blaxter, 2021 ), the Earth Biogenome Project ( Lewin et al, 2018 ), and the 5000 Arthropod Genomes Initiative ( Robinson et al, 2011a ). In addition to establishing new standards for modern large-scale genomics projects and opening avenues for genomic research that were previously only feasible in model organisms across a multitude of species, these projects are creating an opportunity to study genetic variation and address fundamental biological questions at a scope that was simply not possible before.…”

Lagomorpha as a Model Morphological System

“…Analyses based on eight housekeeping genes further confirmed the monophyly of Glires (Kullberg et al, 2006). This was further evidenced by genome level data, including the monophyly of Glires, their close relationship with Primates, Scandentia and Dermoptera; and that all these taxa together formed the clade of Euarchontoglires (=Supraprimates) (Kumar et al, 2013;Foley et al, 2016;Esselstyn et al, 2017;Upham et al, 2019;Genereux et al, 2020).…”

High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox

“…Overall, our carnivoran hybrid assemblies are fairly comparable to those obtained using the classic Illumina-based genome sequencing protocol involving the sequencing of both paired-end and mate-paired libraries ( Li et al, 2010 ). The benefit of adding Nanopore long reads is demonstrated by the fact that our hybrid assemblies are of better quality than all the draft genome assemblies generated using the DISCOVAR de novo protocol based on a PCR-free single Illumina 250 bp paired-end library ( Weisenfeld et al, 2014 ) used in the 200 Mammals Project of the Broad Genome Institute ( Zoonomia Consortium, 2020 ). These results confirm the capacity of the MaSuRCA hybrid assembler to produce high quality assemblies for large and complex genomes by leveraging the power of long Nanopore reads ( Wang et al, 2020 ).…”