PromethION Sequencing and Assembly of the Genome of Micropoecilia picta, a Fish with a Highly Degenerated Y Chromosome. (23rd July 2021)

• Record Type: Journal Article
• Authors: Charlesworth, Deborah; Graham, Chay; Trivedi, Urmi; Gardner, Jim; Bergero, Roberta
• Editors: Yi, Soojin
• Is Part Of: Genome biology and evolution. Volume 13:Number 9(2021)
• Publication Date: 2021-07-23
• Subjects: genome sequence -- genetic degeneration -- sex chromosome; Genomics -- Periodicals; Genes -- Periodicals; 572.8605
• DOI: 10.1093/gbe/evab171
• Languages: English
• ISSNs: 1759-6653

Abstract

Abstract: We here describe sequencing and assembly of both the autosomes and the sex chromosome in Micropoecilia picta, the closest related species to the guppy, Poecilia reticulata . Poecilia ( Micropoecilia ) picta is a close outgroup for studying the guppy, an important organism for studies in evolutionary ecology and in sex chromosome evolution. The guppy XY pair (LG12) has long been studied as a test case for the importance of sexually antagonistic variants in selection for suppressed recombination between Y and X chromosomes. The guppy Y chromosome is not degenerated, but appears to carry functional copies of all genes that are present on its X counterpart. The X chromosomes of M. picta (and its relative Micropoecilia parae ) are homologous to the guppy XY pair, but their Y chromosomes are highly degenerated, and no genes can be identified in the fully Y-linked region. A complete genome sequence of a M. picta male may therefore contribute to understanding how the guppy Y evolved. These fish species' genomes are estimated to be about 750 Mb, with high densities of repetitive sequences, suggesting that long-read sequencing is needed. We evaluated several assembly approaches, and used our results to investigate the extent of Y chromosome degeneration in this species.