Genome Report: Genome of the Amazon Guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation

Abstract

The Amazon guppy, Poecilia bifurca, is a small live-bearing fish. Closely related species, such as P. reticulata, P. picta, and P. parae all share the same sex chromosome system, but with substantial diversity in the degree of Y degeneration and the extent of X chromosome dosage compensation. We built a female (XX) draft genome with 55X coverage of PacBio HiFi data, resulting in a 785 Mb assembly with 94.4% BUSCO completeness. Using this genome, we found that P. bifurca shares the same sex chromosomes as related species and shows substantial Y chromosome degeneration. We combined this with RNA-Seq data and find similar expression of X-linked genes between sexes, revealing that P. bifurca also exhibits complete X chromosome dosage compensation. We further identify 11 putative autosome-to-Y gene duplications, five of which show gene expression in guppy male germ cells.