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Open Access Research article

Functional innovations of three chronological mesohexaploid Brassica rapa genomes

Jungeun Kim12, Jeongyeo Lee1, Jae-Pil Choi1, Inkyu Park13, Kyungbong Yang12, Min Keun Kim4, Young Han Lee4, Ill-Sup Nou5, Dae-Soo Kim1, Sung Ran Min1, Sang Un Park3 and HyeRan Kim12*

Author Affiliations

1 Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea

2 Biosystems & Bioengineering, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea

3 College of Agriculture and Life Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764, Republic of Korea

4 Division of Environment-Friendly Research, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju 660-360, Republic of Korea

5 Department of Horticulture, Sunchon National University, Suncheon 540-742, Republic of Korea

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BMC Genomics 2014, 15:606  doi:10.1186/1471-2164-15-606

Published: 18 July 2014

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.

Conclusion

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.

Keywords:
Brassica rapa; Chronological genomes; Fast-evolving genes; Single-retention genes; Multi-retention genes