Stabilization of hybrid genome and reconstruction of transcriptome network in xBrassicoraphanus

Abstract

Hybridization and polyploidization have facilitated the evolution of many plant species while resulting in speciation and production of novel characteristics to increase fitness in new environments. These phenomena have occurred in various organisms, especially in plants, and the evolution of complex and various sizes of plant genomes has been attributed to polyploidization events. Although increased genomic content and large changes of gene expression levels in polyploid genome provide various advantages for environmental adaptation, most early generated polyploid plants suffer from genomic instability that results in sterility and inviability. xBrassicoraphanus is an intergeneric allopolyploid between Chinese cabbage and radish, which is a rare case of genetic merging two different genus species. Unlike most neoallopolyploid plants, xBrassicoraphanus is fertile and genetically stable, but little is known about the stabilization of hybrid genome between extremely divergent species and the molecular mechanism of transcriptional and epigenetic changes. In this study, I investigated the genomic, transcriptomic and epigenomic changes in a new intergeneric allotetraploid species xBrassicoraphanus. For the genomic analysis, de novo assembly of xBrassicoraphanus genome was performed. Complete set of both parental chromosomes without apparent genome structure changes was observed and hypermethylation of transposable elements by small RNA in trans were proposed. In addition, genome-wide transcriptional changes relative to parental expression are dramatically observed, and the majority of the duplicated genes are adjusted to similar levels due to the high similarity of cis-elements and sharing common transcription factors. This study demonstrates that a certain level of parental genome divergence is helpful to suppress genomic shocks in the early generation of polyploidy and compatibility of regulatory elements would contribute to the massive reconstruction of transcription control network following after transcriptome shock.