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

Plant genomes are smaller than expected despite the ubiquity of polyploidy due to the process of genome downsizing called fractionation. This process causes loss of DNA sequences, including genes, until genomes return to a diploid-like state, though some duplicates remain from the polyploid ancestor. Fractionation can affect the copies of ancestral diploid genomes (i.e., subgenomes) differently, resulting in one being preferentially retained and the other preferentially lost. While previous work suggested fractionation occurs shortly after a polyploidy event, few studies have been able to densely sample descendent genomes from the same whole genome duplication event. The Tripsacinae subtribe of grasses, which includes the genera Tripsacum and Zea and the economically and culturally important maize (Zea mays ssp. mays), originates from an ancient allopolyploid ([~]5-12 MYA). We use publicly available genome assemblies from the Tripsacinae subtribe of grasses to investigate the patterns and timing of fractionation relative to the outgroup sorghum, which does not share the allotetraploidy event. Our results show the majority of fractionation following polyploidy occurred in a common ancestor of modern species and that one subgenome is preferentially retained, in keeping with previous studies of maize. However, Tripsacum retains a greater proportion of duplicate genes (homoeologs) than Zea, potentially related to the fewer chromosomal rearrangements observed in this genus. Multiple, nested deletion events were commonly observed in alignments to a single sorghum reference exon, and some homoeologs show fractionation of different exons across genomes. Further, [~]35% of homoeologous pairs of exons show differential fractionation, where fractionation patterns differ between species. Altogether, this suggests multiple origins of fractionation for a given homoeolog may be common. We demonstrate that fractionation is a much more dynamic process in the Tripsacinae than previously predicted.