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.
Highlights
Comparative genomics can address this challenge by identifying nucleotide positions that have remained unchanged across millions of years of evolution[6], focusing the search for disease-causing variants
By expanding the number of species and making an alignment that is independent of any single reference genome, the Zoonomia Project was designed to detect evolutionary constraint in the eutherian lineage at increased resolution, and to provide genomic resources for over 130 previously uncharacterized species
For nine DISCOVAR assemblies and one pre-existing assembly (the lesser hedgehog tenrec (Echinops telfairi)), we increased contiguity 200-fold (the median scaffold length increased from 90.5 kb to 18.5 megabases (Mb)) through proximity ligation, which uses chromatin interaction data to capture the physical relationships among genomic regions[12]
Summary
In 2011, the 29 Mammals Project[7] identified 12-base-pair (bp) regions of evolutionary constraint that in total comprise 4.2% of the genome, by measuring sequence conservation in humans plus 28 other mammals. For 131 genomes we generated assemblies by performing a single lane of sequencing (2× 250-bp reads) on PCR-free libraries and assembling with DISCOVAR de novo[11] (referred to here as ‘DISCOVAR assemblies’) This method does not require intact cells and uses less than two micrograms of medium-quality DNA (most fragments are over 5 kilobases (kb) in size), which allowed us to include species that are difficult to access We are working on upgrading the assembly of the large treeshrew (Tupaia tana) for the remaining order (Scandentia)
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