title: Functional innovations of three chronological mesohexaploid Brassica rapa genomes.
abstract: BACKGROUND
  The Brassicaceae family is an exemplary model for studying plant polyploidy. The Brassicaceae knowledge-base includes the well-annotated Arabidopsis thaliana reference sequence; well-established evidence for three rounds of whole genome duplication (WGD); and the conservation of genomic structure, with 24 conserved genomic blocks (GBs). The recently released Brassica rapa draft genome provides an ideal opportunity to update our knowledge of the conserved genomic structures in Brassica, and to study evolutionary innovations of the mesohexaploid plant, B. rapa.
  
  
  RESULTS
  Three chronological B. rapa genomes (recent, young, and old) were reconstructed with sequence divergences, revealing a trace of recursive WGD events. A total of 636 fast evolving genes were unevenly distributed throughout the recent and young genomes. The representative Gene Ontology (GO) terms for these genes were 'stress response' and 'development' both through a change in protein modification or signaling, rather than by enhancing signal recognition. In retention patterns analysis, 98% of B. rapa genes were retained as collinear gene pairs; 77% of those were singly-retained in recent or young genomes resulting from death of the ancestral copies, while others were multi-retained as long retention genes. GO enrichments indicated that single retention genes mainly function in the interpretation of genetic information, whereas, multi-retention genes were biased toward signal response, especially regarding development and defense. In the recent genome, 13,302, 5,790, and 20 gene pairs were multi-retained following Brassica whole genome triplication (WGT) events with 2, 3, and 4 homoeologous copies, respectively. Enriched GO-slim terms from B. rapa homomoelogues imply that a major effect of the B. rapa WGT may have been to acquire environmental adaptability or to change the course of development. These homoeologues seem to more frequently undergo subfunctionalization with spatial expression patterns compared with other possible events including nonfunctionalization and neofunctionalization.
  
  
  CONCLUSIONS
  We refined Brassicaceae GB information using the latest genomic resources, and distinguished three chronologically ordered B. rapa genomes. B. rapa genes were categorized into fast evolving, single- and multi-retention genes, and long retention genes by their substitution rates and retention patterns. Representative functions of the categorized genes were elucidated, providing better understanding of B. rapa evolution and the Brassica genus.
authors.forename: Jungeun
authors.initials: J
authors.lastname: Kim
authors.forename: Jeongyeo
authors.initials: J
authors.lastname: Lee
authors.forename: Jae-Pil
authors.initials: JP
authors.lastname: Choi
authors.forename: Inkyu
authors.initials: I
authors.lastname: Park
authors.forename: Kyungbong
authors.initials: K
authors.lastname: Yang
authors.forename: Min Keun
authors.initials: MK
authors.lastname: Kim
authors.forename: Young Han
authors.initials: YH
authors.lastname: Lee
authors.forename: Ill-Sup
authors.initials: IS
authors.lastname: Nou
authors.forename: Dae-Soo
authors.initials: DS
authors.lastname: Kim
authors.forename: Sung Ran
authors.initials: SR
authors.lastname: Min
authors.forename: Sang Un
authors.initials: SU
authors.lastname: Park
authors.affiliation: Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea. kimhr@kribb.re.kr.
authors.forename: HyeRan
authors.initials: H
authors.lastname: Kim
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D005075:Biological Evolution; D001937:Brassica / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics / Q000378:metabolism; D020440:Gene Duplication; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development; D011123:Polyploidy
chemical_list: D010940:Plant Proteins