Comparative Genomics – 200 Mammals – Zoonomia

The 200 Mammals Project started in 2012 with the main goal to understand the human genome, base per base. By comparing more than 240 mammalian genomes and looking at single base resolution, the evolutionary constraint for each base can be measured and is likely to indicate a function for that base. 131 genomes included in the project were generated by us using DISCOVAR-de novo, combined with the 110 mammalian genomes present in NCBI in March 2017. As this data set is analyzed, it will represent the largest eutherian nuclear genome phylogeny and provide the possibility to perform genotype–phenotype correlations across hundreds of mammalian species. It will allow the study of evolution of genome structure, provide reference genomes that can be utilized for species conservation and a very detailed map of evolutionary constraint which can be used with human genome-wide association (GWAS) catalogs and other data sets to investigate patterns of constraint in disease associated regions in any of the mammalian genomes studied. The data set will also allow the study of accelerated regions (genomic regions or positions that may be under positive selection for novel functions) in any of the sequenced mammalian genomes.

Three of the 68 genomes sequenced in the Lindblad-Toh Lab:

Photo by Bryan Padron on Unsplash

Western spotted skunk (Spilogale gracilis)

Photo by Matt Odell on Unsplash

Two-toed sloth (Choloepus didactylus)

Photo by Sridhar Chilimuri on Unsplash

Arctic fox (Vulpes lagopus)

Scientific publications:

Zoonomia Consortium. 2020. A comparative genomics multitool for scientific discovery and conservation. Nature 587, 240–245. doi:10.1038/s41586-020-2876-6

Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I.T., Novak, A.M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., Genereux, D., Johnson, J., Marinescu, V.D., Alföldi, J., Harris, R.S., Lindblad-Toh, K., Haussler, D., Karlsson, E., Jarvis, E.D., Zhang, G., Paten, B., 2020. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587, 246–251.

Lindblad-Toh, K., 2020. What animals can teach us about evolution, the human genome, and human disease. Ups J Med Sci 1–9. doi:10.1080/03009734.2020.1722298

Meadows, J.R.S., Lindblad-Toh, K., 2017. Dissecting evolution and disease using comparative vertebrate genomics. Nat Rev Genet 18, 624–636. doi:10.1038/nrg.2017.51