A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies.
Relatively few indica rice full-length cDNAs were available to aid in the annotation of rice genes. The data presented here described the sequencing and analysis of 10,096 full-length cDNAs from Oryza sativa subspecies indica Guangluai 4. Of them, 9,029 matched rice genomic sequences in publicly-available databases, and 1,200 were identified as new rice genes. Comparison with the knowledge-based Oryza Molecular Biological Encyclopedia japonica cDNA collection indicated that 3,316 (41.6%) of the 7,965 indica-japonica cDNA pairs showed no distinct variations at protein level (2,117 indica-japonica cDNA pairs showed fully identical and 1,199 indica-japonica cDNA pairs showed no frame shift). Moreover, 3,645 (45.8%) of the indica-japonica pairs showed substantial differences at the protein level due to single nucleotide polymorphisms (SNPs), insertions or deletions, and sequence-segment variations between indica and japonica subspecies. Further experimental verifications using PCR screening and quantitative reverse transcriptional PCR revealed unique transcripts for indica subspecies. Comparative analysis also showed that most of rice genes were evolved under purifying selection. These variations might distinguish the phenotypic changes of the two cultivated rice subspecies indica and japonica. Analysis of these cDNAs extends known rice genes and identifies new ones in rice.
Liu
Xiaohui
X
National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China.
Lu
Tingting
T
Yu
Shuliang
S
Li
Ying
Y
Huang
Yuchen
Y
Huang
Tao
T
Zhang
Lei
L
Zhu
Jingjie
J
Zhao
Qiang
Q
Fan
Danlin
D
Mu
Jie
J
Shangguan
Yingying
Y
Feng
Qi
Q
Guan
Jianping
J
Ying
Kai
K
Zhang
Yu
Y
Lin
Zhixin
Z
Sun
Zongxiu
Z
Qian
Qian
Q
Lu
Yuping
Y
Han
Bin
B
D017398:Alternative Splicing; D001483:Base Sequence; D017931:DNA Primers; D018076:DNA, Complementary; D017343:Genes, Plant; D014644:Genetic Variation; D012275:Oryza / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013045:Species Specificity
D017931:DNA Primers; D018076:DNA, Complementary