New Statistical Tools for Allele- or Homeolog-Specific Epigenomics Data, with Applications to Rapid Adaptation of Artificially Synthesized Polyploid Species to Environmental Niches

Rie Inatsugi-Shimizu (EBES), Mark Robinson (IMLS), Kentaro Shimizu (EBES)

Allopolyploidization, or genome duplication with hybridization, is a mechanism of rapid speciation and would be a suitable model to study evolution in action. Artificial allopolyploids in the laboratory have shown rapid genetic changes and epigenetic silencing by DNA methylation in several generations. However, little is known about the evolutionary relevance of allopolyploidization in natural environments. Here, we focus on allotetraploid Arabidopsis kamchatica, which has a broad habitat range from hot sandy shores to cold alpine regions. We have conducted transplantation experiments in five natural sites (alt. 80 m to 2800 m) as well as in controlled chambers for three years. While natural polyploids showed local advantage, synthetic polyploids survived at all conditions, tolerating broader environmental stresses. In addition, rapid increase in fecundity over 3 years supported that this would be a unique experimental evolution system in plants. We developed a new bioinformatic workflow for polyploid RNA-seq analysis, and found that de-silencing was more common than silencing. Thus, we hypothesize that DNA methylation in coding regions may be decreased soon after allopolyploidization and that de-silencing of parent-specific temperature response genes confers increased environmental tolerance, while epigenetic silencing is mainly confined to repetitive sequences. To test this, we will collect genome-wide bisulphite sequencing data from the preserved tissue and develop new statistical tools for homeolog-specific DNA methylome analysis. These tools would be also applicable to other research areas, such as allele-specific methylome in cancer or sexual reproduction.

PhD Student: Stefan Milosavljevic