A robust methodology for assessing differential homeolog contributions to the transcriptomes of allopolyploids

Polyploidy has played a pivotal and recurring role in angiosperm evolution. Allotetraploids arise from hybridization between species and possess duplicated gene copies (homeologs) that serve redundant roles immediately after polyploidization. Although polyploidization is a major contributor to plant evolution, it remains poorly understood.

University of Florida researchers describe an analytical approach for assessing homeolog-specific expression that begins with de novo assembly of parental transcriptomes and effectively (i) reduces redundancy in de novo assemblies, (ii) identifies putative orthologs, (iii) isolates common regions between orthologs, and (iv) assesses homeolog-specific expression using a robust Bayesian Poisson-Gamma model to account for sequence bias when mapping polyploid reads back to parental references. Using this novel methodology, the researchers examine differential homeolog contributions to the transcriptome in the recently formed allopolyploids Tragopogonmirus and T. miscellus (Compositae). Notably, they assess a larger Tragopogon gene set than previous studies of this system. Using carefully identified orthologous regions and filtering biased orthologs, they find in both allopolyploids largely balanced expression with no strong parental bias. These new methods can be used to examine homeolog expression in any tetrapolyploid system without requiring a reference genome.

Tragopogon Triangle

Triangle depicting the relationships between diploid and polyploid Tragopogon species. Diploid individuals occupy the corners of the triangle with polyploids resting between their corresponding diploid progenitors. The polyploid T. mirus is formed with a paternal T. dubius and maternal T. porrifolius. In this study, we are using the short-liguled T. miscellus, which is formed by paternal T. dubius and maternal T. pratensis. There are no naturally occurring polyploids between T. porrifolius and T. pratensis, although these two species do form diploid hybrids in nature.