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

Authors: GAULT, CHRISTINE - Cornell University; KREMLING, KARL - Cornell University; Buckler, Edward - Ed

Submitted to: The Plant Genome
Publication Type: Review Article
Publication Acceptance Date: 7/2/2018
Publication Date: 2/20/2018
Citation: Gault, C., Kremling, K., Buckler IV, E.S. 2018. Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy. The Plant Genome. https://doi.org/10.1101/267682.
DOI: https://doi.org/10.1101/267682

Interpretive Summary: Plants can sometimes undergo whole genome duplication events, which is when their chromosome number doubles in a single generation. The descendants of a plant with doubled chromosomes will shed portions of their genomes over millions of years. Maize and its wild relative Tripsacum share a whole genome duplication event in their recent history. After they evolved into different species, maize and Tripsacum have been shedding portions of their genome independently. It is unknown whether the two species are losing similar genes or whether gene loss happens randomly in each species. This study shows that similar genes in maize and Tripsacum show signatures of functional decay, supporting the idea that gene loss does not happen randomly. The hope is that an increased understanding of the genetic similarities between Tripsacum and maize will lead to better cultivation of maize, a highly valuable crop worldwide.

Technical 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 genes with protein evidence are resisting gene loss in maize and whether their homologs are also resisting gene loss in Tripsacum. 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.