Trio-binned genomes of the woodrats Neotoma bryanti and Neotoma lepida reveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing genes.

Autor: Greenhalgh R; School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA., Holding ML; Department of Natural Resources & Environmental Science, University of Nevada, Reno, Reno, Nevada, USA.; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA., Orr TJ; School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA.; Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA., Henderson JB; Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, USA., Parchman TL; Department of Biology, University of Nevada, Reno, Reno, Nevada, USA., Matocq MD; Department of Natural Resources & Environmental Science, University of Nevada, Reno, Reno, Nevada, USA., Shapiro MD; School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA., Dearing MD; School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA.
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2022 Oct; Vol. 22 (7), pp. 2713-2731. Date of Electronic Publication: 2022 Jun 19.
DOI: 10.1111/1755-0998.13650
Abstrakt: The genomic architecture underlying the origins and maintenance of biodiversity is an increasingly accessible feature of species, due in large part to third-generation sequencing and novel analytical toolsets. Applying these techniques to woodrats (Neotoma spp.) provides a unique opportunity to study how herbivores respond to environmental change. Neotoma bryanti and N. lepida independently achieved a major dietary feat in the aftermath of a natural climate change event: switching to the novel, toxic food source creosote bush (Larrea tridentata). To better understand the genetic mechanisms underlying this ability, we employed a trio binning sequencing approach with a N. bryanti × N. lepida F 1 hybrid, allowing the simultaneous assembly of genomes representing each parental species. The resulting phased, chromosome-level, highly complete haploid references enabled us to explore the genomic architecture of several gene families-cytochromes P450, UDP-glucuronosyltransferases (UGTs), and ATP-binding cassette (ABC) transporters-known to play key roles in the metabolism of naturally occurring toxic dietary compounds. In addition to duplication events in the ABCG and UGT2B subfamilies, we found expansions in three P450 gene families (2A, 2B, 3A), including the evolution of multiple novel gene islands within the 2B and 3A subfamilies, which may have provided the crucial substrate for dietary adaptation. Our assemblies demonstrate that trio binning from an F 1 hybrid rodent effectively recovers parental genomes from species that diverged more than a million years ago.
(© 2022 John Wiley & Sons Ltd.)
Databáze: MEDLINE
Externí odkaz: