High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages ofￂ polyploid genome evolution

• Published in: The Plant journal : for cell and molecular biology Vol. 91; no. 2; p. 278
• Main Authors: Kasianov, Artem S, Klepikova, Anna V, Kulakovskiy, Ivan V, Gerasimov, Evgeny S, Fedotova, Anna V, Besedina, Elizaveta G, Kondrashov, Alexey S, Logacheva, Maria D, Penin, Aleksey A
• Format: Journal Article
• Language: English
• Published: Oxford Blackwell Publishing Ltd 01.07.2017
• Subjects: Assembly; Asymmetry; Binding sites; Biological evolution; Developmental stages; Divergence; Evolution & development; Evolutionary genetics; Gene duplication; Gene expression; Gene regulation; Genes; Genomes; Light effects; Organs; Photosynthesis; Polyploidy; Promoters; Regulatory sequences; Speciation; Temperature effects; Transcription factors
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.13563

Summary Polyploidization and subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant genome evolution. Capsella bursa-pastoris, a widespread ruderal plant, is a recent allotetraploid and, thus, is an ideal model organism for studying early changes following polyploidization. We constructed a high-quality assembly of C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmental stages (available online at http://travadb.org/browse/Species=Cbp). We demonstrate that expression of homeologs is mostly symmetric between subgenomes, and identify a set of homeolog pairs with discordant expression. Comparison of promoters within such pairs revealed emerging asymmetry of regulatory elements. Among them there are multiple binding sites for transcription factors controlling the regulation of photosynthesis and plant development by light (PIF3, HY5) and cold stress response (CBF). These results suggest that polyploidization in C. bursa-pastoris enhanced its plasticity of response to light and temperature, and allowed substantial expansion of its distribution range. Significance Statement The Capsella genus is an emerging model for studying phenotypic evolution, speciation and polyploidization. Here we assembled the Capsella bursa-pastoris genome and analyzed the transcriptome and regulatory elements in the sub-genomes, thereby defining a set of genes that were likely targets of functional divergence after polyploidization.