Ongoing rapid evolution of a post-Y region revealed by chromosome-scale genome assembly of a hexaploid monoecious persimmon (Diospyros kaki)

Abstract

Sex chromosomes have evolved independently in many plant lineages. They have often undergone rapid structural degeneration and extension of non-recombining regions, which is conventionally considered to be strongly associated with the expression of sexually dimorphic traits. In this study, we assembled a monoecious hexaploid persimmon (Diospyros kaki) in which the Y chromosome had lost its function in male determination. Comparative genomic analysis among D. kaki and its dioecious relatives revealed that the non-functional Y chromosome (Ym) via silencing of the sex-determining gene, OGI, arose approximately two million years ago. Comparative analyses of the whole X and Ym chromosomes suggested that the non-functional male-specific region of the Y-chromosome (MSY), or post-MSY, retained certain conserved characteristics of the original functional MSY. Specifically, comparison of the functional MSY in D. lotus and the non-functional post-MSY in D. kaki indicated that the post-MSY had been rapidly rearranged mainly via ongoing transposable element bursts, as well as in the functional MSY. These results suggest a novel interpretation that the rapid evolution of the post-MSY (and possibly also MSYs in dioecious Diospyros species) might reflect the ancestral genomic properties of these regions, rather than the evolution of male-determining functions and/or sexually dimorphic traits.