title: Evolutionary trajectory of phytoalexin biosynthetic gene clusters in rice.
abstract: Plants frequently possess operon-like gene clusters for specialized metabolism. Cultivated rice, Oryza sativa, produces antimicrobial diterpene phytoalexins represented by phytocassanes and momilactones, and the majority of their biosynthetic genes are clustered on chromosomes 2 and 4, respectively. These labdane-related diterpene phytoalexins are biosynthesized from geranylgeranyl diphosphate via ent-copalyl diphosphate or syn-copalyl diphosphate. The two gene clusters consist of genes encoding diterpene synthases and chemical-modification enzymes including P450s. In contrast, genes for the biosynthesis of gibberellins, which are labdane-related phytohormones, are scattered throughout the rice genome similar to other plant genomes. The mechanism of operon-like gene cluster formation remains undefined despite previous studies in other plant species. Here we show an evolutionary insight into the rice gene clusters by a comparison with wild Oryza species. Comparative genomics and biochemical studies using wild rice species from the AA genome lineage, including Oryza barthii, Oryza glumaepatula, Oryza meridionalis and the progenitor of Asian cultivated rice Oryza rufipogon indicate that gene clustering for biosynthesis of momilactones and phytocassanes had already been accomplished before the domestication of rice. Similar studies using the species Oryza punctata from the BB genome lineage, the distant FF genome lineage species Oryza brachyantha and an outgroup species Leersia perrieri suggest that the phytocassane biosynthetic gene cluster was present in the common ancestor of the Oryza species despite the different locations, directions and numbers of their member genes. However, the momilactone biosynthetic gene cluster evolved within Oryza before the divergence of the BB genome via assembly of ancestral genes.
authors.affiliation: Department of Biosciences, Teikyo University, Toyosatodai 1-1, Utsunomiya, Tochigi, 320-8551, Japan.|Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Miyamoto
authors.affiliation: Plant Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Fujita
authors.affiliation: Plant Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Shenton
authors.affiliation: Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
authors.forename: Shota
authors.initials: S
authors.lastname: Akashi
authors.affiliation: Faculty of Agriculture, Yamagata University, Wakaba-cho 1-23, Tsuruoka, Yamagata, 997-8555, Japan.
authors.forename: Chizu
authors.initials: C
authors.lastname: Sugawara
authors.affiliation: Faculty of Agriculture, Yamagata University, Wakaba-cho 1-23, Tsuruoka, Yamagata, 997-8555, Japan.
authors.forename: Arisa
authors.initials: A
authors.lastname: Sakai
authors.affiliation: Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo, 183-8509, Japan.
authors.forename: Kiyotaka
authors.initials: K
authors.lastname: Horie
authors.affiliation: Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo, 183-8509, Japan.|College of Agriculture, Ibaraki University, Ami-machi Chuo 3-21-1, Ibaraki, 300-0393, Japan.
authors.forename: Morifumi
authors.initials: M
authors.lastname: Hasegawa
authors.affiliation: Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu, Tokyo, 183-8509, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kawaide
authors.affiliation: Faculty of Agriculture, Yamagata University, Wakaba-cho 1-23, Tsuruoka, Yamagata, 997-8555, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Mitsuhashi
authors.affiliation: Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Nojiri
authors.affiliation: Department of Biosciences, Teikyo University, Toyosatodai 1-1, Utsunomiya, Tochigi, 320-8551, Japan.
authors.forename: Hisakazu
authors.initials: H
authors.lastname: Yamane
authors.affiliation: Plant Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
authors.forename: Nori
authors.initials: N
authors.lastname: Kurata
authors.affiliation: Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan. ukokada@mail.ecc.u-tokyo.ac.jp.
authors.forename: Kazunori
authors.initials: K
authors.lastname: Okada
authors.affiliation: Faculty of Agriculture, Yamagata University, Wakaba-cho 1-23, Tsuruoka, Yamagata, 997-8555, Japan. toyomasu@tds1.tr.yamagata-u.ac.jp.
authors.forename: Tomonobu
authors.initials: T
authors.lastname: Toyomasu
mesh_terms: D004224:Diterpenes / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D005810:Multigene Family / Q000235:genetics / Q000502:physiology; D012275:Oryza / Q000235:genetics / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D012717:Sesquiterpenes / Q000378:metabolism*; D000094162:Phytoalexins
chemical_list: D004224:Diterpenes; D010940:Plant Proteins; D012717:Sesquiterpenes; D000094162:Phytoalexins
keywords: biosynthesis; diterpenoid; evolution; operon-like gene cluster; rice