A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids

Genetics
J Lucas BoatwrightW Brad Barbazuk

Abstract

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. We 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, we examine differential homeolog contributions to the transcriptome in the recently formed allopolyploids Tragopogon mirus and T. miscellus (Compositae). Notably, we assess a larger Tragopogon gene set than previous studies of this system. Using carefully identified orthologous regions and filtering biased orthologs, we find in both allopolyploids largely balanced expression with no strong parental bias. The...Continue Reading

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Citations

Dec 28, 2018·Briefings in Bioinformatics·Tony C Y KuoJun Sese
Jul 19, 2021·BMC Genomics·Stefan MilosavljevicMark D Robinson
Jun 22, 2021·The Plant Journal : for Cell and Molecular Biology·Marek GlombikDavid Kopecky

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