title: Genome-wide identification and phylogenetic analysis of the chalcone synthase gene family in rice.
abstract: The enzymes of the chalcone synthase family are also known as type III polyketide synthases (PKS), and produce a series of secondary metabolites in bacteria, fungi and plants. In a number of plants, genes encoding PKS comprise a large multigene family. Currently, detailed reports on rice (Oryza sativa) PKS (OsPKS) family genes and tissue expression profiling are limited. Here, 27 candidate OsPKS genes were identified in the rice genome,and 23 gene structures were confirmed by EST and cDNA sequencing; phylogenetic analysis has indicated that these 23 OsPKS members could be clustered into three groups (I-III). Comparative analysis has shown OsPKS08 and OsPKS26 could be classified with the CHS genes of other species. Two members OsPKS10 and OsPKS21 were grouped into anther specific chalcone synthase-like (ASCL) clade. Intron/exon structure analysis revealed that nearly all of the OsPKS members contained one phase-1 intron at a conserved Cys. Analysis of chromosomal localization and genome distribution showed that some of the members were distributed on a chromosome as a cluster. Expression data exhibited widespread distribution of the rice OsPKS gene family within plant tissues, suggesting functional diversification of the OsPKS genes. Our results will contribute to future study of the complexity of the OsPKS gene family in rice.
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nangchang, 330045, China.|Collaboration Center for Double Cropping Rice Modernization Production, Nanchang, 330045, Jiangxi, China.|Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410000, China.
authors.forename: Lifang
authors.initials: L
authors.lastname: Hu
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nangchang, 330045, China.|Collaboration Center for Double Cropping Rice Modernization Production, Nanchang, 330045, Jiangxi, China.|Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410000, China.
authors.forename: Haohua
authors.initials: H
authors.lastname: He
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nangchang, 330045, China.
authors.forename: Changlan
authors.initials: C
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nangchang, 330045, China.
authors.forename: Xiaosong
authors.initials: X
authors.lastname: Peng
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nangchang, 330045, China.
authors.forename: Junru
authors.initials: J
authors.lastname: Fu
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nangchang, 330045, China.
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: He
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nangchang, 330045, China.
authors.forename: Xiaorong
authors.initials: X
authors.lastname: Chen
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nangchang, 330045, China.
authors.forename: Linjuan
authors.initials: L
authors.lastname: Ouyang
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nangchang, 330045, China.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Bian
authors.affiliation: School of Sciences, Jiangxi Agricultural University, Nanchang Economic and Technological Development District, Nanchang, 330045, Jiangxi, China. lsq_hn306@163.com.
authors.forename: Shiqiang
authors.initials: S
authors.lastname: Liu
mesh_terms: D000217:Acyltransferases / Q000235:genetics*; D002874:Chromosome Mapping; D030561:Databases, Nucleic Acid; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D007438:Introns / Q000235:genetics; D005810:Multigene Family; D012275:Oryza / Q000201:enzymology* / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins; D000217:Acyltransferases; C020141:flavanone synthetase
keywords: Gene family; OsPKS; Phylogenetic analysis; Rice