Identification of Homeolog-Specific Expression Change in Allopolyploid Species Arabidopsis kamchatica from RNA-Seq Data

Allopolyploid originated in reunification of evolutionary divergent genomes, and the allopolyploidies have been researched to understand adaptation mechanisms in ecology since they tend to have higher habitat diversity than parental species. Allotetraploid Arabidopsis kamchatica lives from East Asia to North America, which includes habitats of both its parental species A. lyrata and A. halleri. The high similarity of the parental genome sequences prevents the genome-wide study to understand the mechanisms of the wide range of the habitat. We here developed a homeolog-specific expression observation procedure on A. kamchatica, which consists of a measurement of homeolog-specific expression levels with RNA-seq and a statistical analysis of homeolog expression specificity alterations induced by the environmental change. We performed RNA-seq from A. kamchatica under different conditions, and our method identified that 78% of the reads were trustable to measure homeolog-specific expressions. Estimated homeolog expression levels based on the reads have high consistency with the experimental results measured by pyrosequencing. The comparison of the expression levels over the conditions shows differentially expressed genes and condition specific homeolog expressions.