title: Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.
abstract: This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.
authors.affiliation: Department of Life Science, The Catholic University of Korea, Bucheon, 420-743, Korea.
authors.forename: Young-Min
authors.initials: YM
authors.lastname: Jeong
authors.affiliation: Epigenomics Research Center of Genome Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.affiliation: Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: Byung Ohg
authors.initials: BO
authors.lastname: Ahn
authors.affiliation: Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: Mijin
authors.initials: M
authors.lastname: Oh
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.affiliation: Department of Life Science, The Catholic University of Korea, Bucheon, 420-743, Korea.
authors.forename: Hee
authors.initials: H
authors.lastname: Chung
authors.affiliation: Epigenomics Research Center of Genome Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.
authors.forename: Seongmun
authors.initials: S
authors.lastname: Jeong
authors.affiliation: Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Korea.
authors.forename: Ki-Byung
authors.initials: KB
authors.lastname: Lim
authors.affiliation: Department of Life Science, Sahmyook University, Seoul, 139-800, Korea.
authors.forename: Yoon-Jung
authors.initials: YJ
authors.lastname: Hwang
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea.
authors.forename: Goon-Bo
authors.initials: GB
authors.lastname: Kim
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea.
authors.forename: Seunghoon
authors.initials: S
authors.lastname: Baek
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea.
authors.forename: Sang-Bong
authors.initials: SB
authors.lastname: Choi
authors.affiliation: SeqGenesis, Daejeon, 305-343, Korea.
authors.forename: Dae-Jin
authors.initials: DJ
authors.lastname: Hyung
authors.affiliation: SeqGenesis, Daejeon, 305-343, Korea.
authors.forename: Seung-Won
authors.initials: SW
authors.lastname: Lee
authors.affiliation: Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: Seong-Han
authors.initials: SH
authors.lastname: Sohn
authors.affiliation: Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: Soo-Jin
authors.initials: SJ
authors.lastname: Kwon
authors.affiliation: Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: Mina
authors.initials: M
authors.lastname: Jin
authors.affiliation: Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: Young-Joo
authors.initials: YJ
authors.lastname: Seol
authors.affiliation: Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 565-852, Korea.
authors.forename: Won Byoung
authors.initials: WB
authors.lastname: Chae
authors.affiliation: Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 565-852, Korea.
authors.forename: Keun Jin
authors.initials: KJ
authors.lastname: Choi
authors.affiliation: Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
authors.affiliation: Department of Life Science, The Catholic University of Korea, Bucheon, 420-743, Korea. yuheeju@catholic.ac.kr.
authors.forename: Hee-Ju
authors.initials: HJ
authors.lastname: Yu
authors.affiliation: Department of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea. munjh@mju.ac.kr.
authors.forename: Jeong-Hwan
authors.initials: JH
authors.lastname: Mun
mesh_terms: D001937:Brassica / Q000235:genetics; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D055028:Comparative Genomic Hybridization; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D031224:Raphanus / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant