title: High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution.
abstract: 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.
authors.affiliation: A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.|N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia.
authors.forename: Artem S
authors.initials: AS
authors.lastname: Kasianov
authors.affiliation: A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.|Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Klepikova
authors.affiliation: N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia.|Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia.|Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Building 3, Moscow, 143026, Russia.
authors.forename: Ivan V
authors.initials: IV
authors.lastname: Kulakovskiy
authors.affiliation: A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.|Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia.|Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
authors.forename: Evgeny S
authors.initials: ES
authors.lastname: Gerasimov
authors.affiliation: A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Fedotova
authors.affiliation: Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.
authors.forename: Elizaveta G
authors.initials: EG
authors.lastname: Besedina
authors.affiliation: A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.|Department of Ecology and Evolution, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, MI, USA.
authors.forename: Alexey S
authors.initials: AS
authors.lastname: Kondrashov
authors.affiliation: A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.|Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia.|Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlevskaya str, Kazan, 420008, Russia.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Logacheva
authors.affiliation: A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.|Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia.|Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
authors.forename: Aleksey A
authors.initials: AA
authors.lastname: Penin
mesh_terms: D029687:Capsella / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D011123:Polyploidy; D012045:Regulatory Sequences, Nucleic Acid
keywords: 
  Capsella bursa-pastoris
  ; RNA-seq; genome assembly; homeologs; polyploidy; regulatory elements