title: [Bioinformatics analysis of the expansin gene family in rice].
abstract: Expansin refers to a family of nonenzymatic proteins found in the plant cell wall with important roles in plant cell growth, developmental processes, and resistance to stress. Whole rice genome sequencing revealed that it contains 58 expansin genes, which belong to 4 subfamilies (A (34), B (19), LA (4) and LB (1)). All the genes were located on 10 of 12 rice chromosomes where several subfamily members clustered. Each of expansin genes ranged from 687 bp to 1128 bp in size. Sequence alignment showed that all expansins had three structural domains with two conserved amino acids of cystine in N-terminus and tryptophan in C-terminus. The amino acid identity of members among different subfamilies was less than 35%, while that among the same subfamily was more than 35%. Most genes of A subfamily had 1 or 2 introns, while genes of B, LA and LB subfamily had 3, 4 and 4 introns, respectively. Statistics analysis of codon usage showed that expansins in rice have 26 high-frequency codons which are more biased than those in other species. These bioinformatics findings will be helpful for the further study of the function and evolution of expansin genes.
authors.affiliation: National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Shi
authors.affiliation: National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Xu
authors.affiliation: National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China.
authors.forename: Haoyang
authors.initials: H
authors.lastname: Li
authors.affiliation: National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Xu
authors.affiliation: National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China.
authors.forename: Jichen
authors.initials: J
authors.lastname: Xu
mesh_terms: D000595:Amino Acid Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D011487:Protein Conformation
chemical_list: D010940:Plant Proteins; C095825:expansin protein, plant