Shared and Species-Specific Patterns of Nascent Y Chromosome Evolution in Two Guppy Species

Abstract

Sex chromosomes form once recombination is halted around the sex-determining locus between a homologous pair of chromosomes, resulting in a male-limited Y chromosome. We recently characterized the nascent sex chromosome system in the Trinidadian guppy (<i>Poecilia</i><i>reticulata</i>). The guppy Y is one of the youngest animal sex chromosomes yet identified, and therefore offers a unique window into the early evolutionary forces shaping sex chromosome formation, particularly the rate of accumulation of repetitive elements and Y-specific sequence. We used comparisons between male and female genomes in <i>P. reticulata</i> and its sister species, Endler&rsquo;s guppy (<i>P. wingei</i>), which share an ancestral sex chromosome, to identify male-specific sequences and to characterize the degree of differentiation between the X and Y chromosomes. We identified male-specific sequence shared between <i>P. reticulata</i> and <i>P. wingei</i> consistent with a small ancestral non-recombining region. Our assembly of this Y-specific sequence shows substantial homology to the X chromosome, and appears to be significantly enriched for genes implicated in pigmentation. We also found two plausible candidates that may be involved in sex determination. Furthermore, we found that the <i>P. wingei</i> Y chromosome exhibits a greater signature of repetitive element accumulation than the <i>P. reticulata</i> Y chromosome. This suggests that Y chromosome divergence does not necessarily correlate with the time since recombination suppression. Overall, our results reveal the early stages of Y chromosome divergence in the guppy.