title: The radish genome and comprehensive gene expression profile of tuberous root formation and development.
abstract: Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.
authors.affiliation: Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Mitsui
authors.affiliation: Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan.
authors.forename: Michihiko
authors.initials: M
authors.lastname: Shimomura
authors.affiliation: Junior College of Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Komatsu
authors.affiliation: Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan.
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Namiki
authors.affiliation: Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
authors.forename: Mari
authors.initials: M
authors.lastname: Shibata-Hatta
authors.affiliation: Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
authors.forename: Misaki
authors.initials: M
authors.lastname: Imai
authors.affiliation: National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Katayose
authors.affiliation: National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Mukai
authors.affiliation: National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kanamori
authors.affiliation: National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan.
authors.forename: Kanako
authors.initials: K
authors.lastname: Kurita
authors.affiliation: Sakata Seed Corporation, 2-7-1, Nakamachidai, Tuzuki-ku, Yokohama, 224-0041, Japan.
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Kagami
authors.affiliation: Sakata Seed Corporation, 2-7-1, Nakamachidai, Tuzuki-ku, Yokohama, 224-0041, Japan.
authors.forename: Akihito
authors.initials: A
authors.lastname: Wakatsuki
authors.affiliation: Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan.
authors.forename: Hajime
authors.initials: H
authors.lastname: Ohyanagi
authors.affiliation: Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ikawa
authors.affiliation: 1] Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan [2] National Institute for Agro-Environmental Science, 3-1-3, Tukuba, 305-8604, Japan.
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Minaka
authors.affiliation: Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
authors.forename: Kunihiro
authors.initials: K
authors.lastname: Nakagawa
authors.affiliation: Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Shiwa
authors.affiliation: 1] Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan [2] National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan.
authors.forename: Takuji
authors.initials: T
authors.lastname: Sasaki
mesh_terms: D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018745:Genome, Plant; D018517:Plant Roots / Q000254:growth & development*; D031224:Raphanus / Q000235:genetics*