Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy

Abstract

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 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 under purifying selection. Here we present high quality de novo transcriptome assemblies for two species: Tripsacum dactyloides and Tripsacum floridanum. Genes with experimental protein evidence in maize were good candidates for genes under purifying selection 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 GC content, higher gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their Tripsacum homologs. These results indicate that gene loss is occurring in a similar fashion 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, an highly valuable crop worldwide.\n\nCore ideasO_LIMaize genes with protein evidence have higher expression and GC content\nC_LIO_LITripsacum homologs of maize genes exhibit the same trends as in maize\nC_LIO_LIMaize proteome genes have more highly correlated gene expression with Tripsacum\nC_LIO_LIExpression dominance for homeologs occurs similarly between maize and Tripsacum\nC_LIO_LIA similar set of genes may be decaying into pseudogenes in maize and Tripsacum\nC_LI