title: Rapid turnover of antimicrobial-type cysteine-rich protein genes in closely related Oryza genomes.
abstract: Defensive and reproductive protein genes undergo rapid evolution. Small, cysteine-rich secreted peptides (CRPs) act as antimicrobial agents and function in plant intercellular signaling and are over-represented among reproductively expressed proteins. Because of their roles in defense, reproduction and development and their presence in multigene families, CRP variation can have major consequences for plant phenotypic and functional diversification. We surveyed the CRP genes of six closely related Oryza genomes comprising Oryza sativa ssp. japonica and ssp. indica, Oryza glaberrima and three accessions of Oryza rufipogon to observe patterns of evolution in these gene families and the effects of variation on their gene expression. These Oryza genomes, like other plant genomes, have accumulated large reservoirs of CRP sequences, comprising 26 groups totaling between 676 and 843 genes, in contrast to antimicrobial CRPs in animal genomes. Despite the close evolutionary relationships between the genomes, we observed rapid changes in number and structure among CRP gene families. Many CRP sequences are in gene clusters generated by local duplications, have undergone rapid turnover and are more likely to be silent or specifically expressed. By contrast, conserved CRP genes are more likely to be highly and broadly expressed. Variable CRP genes created by repeated duplication, gene modification and inactivation can gain new functions and expression patterns in newly evolved gene copies. For the CRP proteins, the process of gain/loss by deletion or duplication at gene clusters seems to be an important mechanism in evolution of the gene families, which also contributes to their expression evolution.
authors.affiliation: Plant Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Shenton
authors.affiliation: Plant Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan.|Mitsubishi Space Software Co. Ltd., Tsukuba Mitsui Building 14F, 1-6-1, Takezono, Tsukuba, Ibaraki, 305-0032, Japan.
authors.forename: Hajime
authors.initials: H
authors.lastname: Ohyanagi
authors.affiliation: National Center for Gene Research, Chinese Academy of Sciences, Shanghai, 500 Caobao Road, Shanghai, 200233, China.
authors.forename: Zi-Xuan
authors.initials: ZX
authors.lastname: Wang
authors.affiliation: Comparative Genomics Laboratory, National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan.|Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Hulic Kamiyacho, 4-3-13 Toranomon, Minatoku, Tokyo, 105-0001, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.affiliation: Comparative Genomics Laboratory, National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan.|Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Hulic Kamiyacho, 4-3-13 Toranomon, Minatoku, Tokyo, 105-0001, Japan.
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.affiliation: Plant Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan.
authors.forename: Toshifumi
authors.initials: T
authors.lastname: Nagata
authors.affiliation: National Center for Gene Research, Chinese Academy of Sciences, Shanghai, 500 Caobao Road, Shanghai, 200233, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.affiliation: National Center for Gene Research, Chinese Academy of Sciences, Shanghai, 500 Caobao Road, Shanghai, 200233, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Han
authors.affiliation: Plant Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan. nkurata@nig.ac.jp.|Department of Genetics, School of Life Sciences, Graduate University of Advanced Studies, SOKENDAI, Yata 1111, Mishima, 411-8540, Japan. nkurata@nig.ac.jp.|Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Hulic Kamiyacho, 4-3-13 Toranomon, Minatoku, Tokyo, 105-0001, Japan. nkurata@nig.ac.jp.
authors.forename: Nori
authors.initials: N
authors.lastname: Kurata
mesh_terms: D000890:Anti-Infective Agents; D003545:Cysteine / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011110:Polymorphism, Genetic; D017423:Sequence Analysis, RNA; D013045:Species Specificity
chemical_list: D000890:Anti-Infective Agents; D010940:Plant Proteins; D003545:Cysteine
keywords: CRP; Cysteine; Evolution; Gene cluster; Oryza
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