Genome-wide analysis of cyclin family in rice (Oryza Sativa L.).
The cyclins together with highly conserved cyclin-dependent kinases regulate cell cycle progression in plants. Although extensive and systematic study on cell cycle mechanisms and cyclin functions in yeasts and animals has been carried out, only a small number of plant cyclins have been characterized and classified functionally and phylogenetically. We identified several types of cyclin genes in the rice genome and characterized them by phylogenetic, tandem and segmental duplications analyses. Our results indicated that there were at least 49 predicted rice cyclin genes in the rice genome, and they were distributed on 12 chromosomes. Of these cyclins, one possessed only cyclin_C domain and no cyclin_N domain, and the remaining 48 cyclins with cyclin_N domains were classified as nine types based on evolutionary relationships. Eight of these nine types were common between rice and Arabidopsis, whereas only one, known as F-type cyclins, was unique to rice. No homologues of the F-type cyclins in plants could be retrieved from the public databases, and reverse transcription-PCR analysis supported an existence of the F-type cyclin genes. Sequence alignment suggested that the cyclin genes in the rice genome experienced a mass of gene tandem and segmental duplications occurred on seven chromosomes related to the origins of new cyclin genes. Our study provided an opportunity to facilitate assessment and classification of new members, serving as a guide for further functional elucidation of rice cyclins.
La
Honggui
H
Rice Functional Genomics, Joint Laboratory of Temasek Life Sciences Laboratory of Singapore and Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, 100101, Beijing, China.
Li
Jun
J
Ji
Zhendong
Z
Cheng
Yanjun
Y
Li
Xiuli
X
Jiang
Shuye
S
Venkatesh
Prasanna Nori
PN
Ramachandran
Srinivasan
S
D029681:Arabidopsis Proteins / Q000235:genetics; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D016213:Cyclins / Q000145:classification / Q000235:genetics*; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D005810:Multigene Family; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D020133:Reverse Transcriptase Polymerase Chain Reaction
D029681:Arabidopsis Proteins; C503669:CCNF protein, human; D016213:Cyclins