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

Area of Science:

• Genomics
• Evolutionary Biology
• Plant Science

Background:

• Whole-genome duplication events in plants can lead to gene loss.
• Maize and its sister genus share an ancient genome duplication event.
• Limited genomic resources exist for the sister genus, hindering comparative studies.

Purpose of the Study:

• To investigate gene loss and pseudogenization patterns in maize and its sister genus.
• To determine if similar genes have resisted decay into pseudogenes in both genera.
• To provide high-quality genomic resources for understanding grass evolution.

Main Methods:

• De novo transcriptome assemblies for two species: Zea mays and Tripsacum dactyloides.
• Identification of maize genes with experimental protein evidence as candidates for conserved genes.
• Comparative analysis of gene expression levels, GC content, and conservation between protein-encoding and untranslated transcripts and their homologs.

Main Results:

• Protein-encoding maize transcripts and their homologs exhibit higher guanine-cytosine (GC) content.
• Genes with protein evidence show higher and more conserved expression levels compared to untranslated transcripts.
• Homologs of protein-encoding maize genes also appear to resist gene loss in the sister genus.

Conclusions:

• Similar sets of genes may be undergoing decay into pseudogenes in both maize and its sister genus following ancient polyploidy.
• The findings suggest conserved mechanisms of gene loss resistance in grasses.
• The generated transcriptome assemblies serve as valuable genomic resources for maize evolution research.