Maize and wild relatives show distinct patterns of genome downsizing following polyploidy

Abstract

Repeated cycles of polyploidy and gene loss during diploidization have shaped plant genomes over evolutionary time. This loss of gene sequence post-polyploidy is known as fractionation. Gene duplicates (i.e., homoeologs) from each ancestral diploid genome (i.e., subgenome) may fractionate differently, resulting in one subgenome being preferentially retained. Previous work suggests fractionation occurs shortly after a polyploidy event. Yet, few studies have explicitly compared genome-wide fractionation patterns across genera sharing the same whole genome duplication (WGD) to clarify how patterns of fractionation distinguish species over time. The Tripsacinae subtribe of grasses, which includes the genera Tripsacum and Zea, share an ancient allotetraploidy event ~5-12 MYA. Using publicly available genome assemblies for the Tripsacinae subtribe including wild lineages and the domesticate maize, we investigate patterns of fractionation. Across genomes, the majority of fractionation is shared across species and one subgenome is preferentially retained. However, ~35% of exons were fractionated differently across species, with significantly more differences between genomes of Tripsacum and Zea. We found no support of incomplete lineage sorting explaining fractionation differences across genera. Rather, the most striking trend is Tripsacum retaining a substantially greater proportion of homoeolog pairs than Zea where gene loss has been more prevalent.