Tripsacum De novo Transcriptome Assemblies Reveal Parallel Gene Evolution with Maize after Ancient Polyploidy

Plant genomes reduce in size following a whole-genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize (Zea mays L.) and its sister genus, Tripsacum, share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for Tripsacum exist, it is unknown whether Tripsacum grasses and maize have maintained a similar set of genes that have resisted decay into pseudogenes. Here we present high-quality de novo transcriptome assemblies for two species: Tripsacum dactyloides (L.) L. and T. floridanum Porter ex Vasey. Genes with experimental protein evidence in maize were good candidates for genes resistant to pseudogenization in both genera because pseudogenes by definition do not produce protein. We tested whether 15,160 maize genes with protein evidence are resisting gene loss and whether their Tripsacum homologs are also resisting gene loss. Protein-encoding maize transcripts and their Tripsacum homologs have higher guanine-cytosine (GC) content, higher gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their Tripsacum homologs. These results suggest that similar genes may be decaying into pseudogenes in both genera after a shared ancient polyploidy event. The Tripsacum transcriptome assemblies provide a high-quality genomic resource that can provide insight into the evolution of maize, a highly valuable crop worldwide.