High quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution. Capsella bursa-pastoris cultivar:msu-wt

Polyploidization and subsequent sub- and neofunctionalization of duplicated genes is a major mechanism of plant genome evolution. Capsella bursa-pastoris, a very widespread ruderal plant, is a recent (~ 500 kya) allotetraploid and thus is an ideal model for investigation of early genomic changes subsequent to polyploidization. We report here high quality genome assembly of Capsella bursa-pastoris and transcriptome atlas covering a broad sampling of tissues and developmental stages. We demonstrate that expression of homeologs is mostly symmetric between subgenomes and define a set of genes that show discordant expression (i.e. one homeolog has significantly higher expression than the other). Comparison of promoters of homeologs showed prevalent emergence of new regulatory elements in such genes. Among these regulatory elements the binding sites for transcription factors controlling regulation of photosynthesis and plant development by light (PIF3, HY5, TOE1, TOE2) are prevalent. This suggests that polyploidization in C. bursa-pastoris resulted in enhanced plasticity of response to light being the key factor that allowed it to expand greatly its distribution range.