Genomic survey, characterization and expression profile analysis of the peptide transporter family in rice (Oryza sativa L.).
BACKGROUND
Peptide transporter (PTR) family whose member can transport di-/tripeptides and nitrate is important for plant growth and development. Although the rice (Oryza sativa L.) genome has been sequenced for a few years, a genomic survey, characterization and expression profile analysis of the PTR family in this species has not been reported.


RESULTS
In this study, we report a comprehensive identification, characterization, phylogenetic and evolutionary analysis of 84 PTR family members in rice (OsPTR) as well as their whole-life expression patterns. Chromosomal distribution and sequence analysis indicate that nearly 70% of OsPTR members are involved in the tandem and segmental duplication events. It suggests that genome duplication might be a major mechanism for expansion of this family. Highly conserved motifs were identified in most of the OsPTR members. Meanwhile, expression profile of OsPTR genes has been analyzed by using Affymetrix rice microarray and real-time PCR in two elite hybrid rice parents, Minghui 63 and Zhenshan 97. Seven genes are found to exhibit either preferential or tissue-specific expression during different development stages of rice. Under phytohormone (NAA, GA3 and KT) and light/dark treatments, 14 and 17 OsPTR genes are differentially expressed respectively. Ka/Ks analysis of the paralogous OsPTR genes indicates that purifying selection plays an important role in function maintenance of this family.


CONCLUSIONS
These investigations add to our understanding of the importance of OsPTR family members and provide useful reference for selecting candidate genes for functional validation studies of this family in rice.
Zhao
Xiaobo
X
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, China. zxb018@webmail.hzau.edu.cn
Huang
Jianyan
J
Yu
Huihui
H
Wang
Lei
L
Xie
Weibo
W
D000595:Amino Acid Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D016000:Cluster Analysis; D003624:Darkness; D020440:Gene Duplication / Q000187:drug effects; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D026901:Membrane Transport Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000494:pharmacology; D036226:Seedlings / Q000187:drug effects / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
D026901:Membrane Transport Proteins; D010937:Plant Growth Regulators; C043912:peptide permease