A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies

文献类型： 外文期刊

第一作者： Liu, Xiaohui

作者： Liu, Xiaohui;Lu, Tingting;Yu, Shuliang;Li, Ying;Huang, Yuchen;Huang, Tao;Zhang, Lei;Zhu, Jingjie;Zhao, Qiang;Fan, Danlin;Mu, Jie;Shangguan, Yingying;Feng, Qi;Guan, Jianping;Ying, Kai;Zhang, Yu;Lin, Zhixin;Sun, Zongxiu;Qian, Qian;Lu, Yuping;Han, Bin

作者机构：

关键词： comparative analysis;full-length cDNA;Indica and japonica rice;Oryza sativa;transcriptome;ARABIDOPSIS-THALIANA;GENOME ANNOTATION;FUNCTIONAL ANNOTATION;BRASSICA-OLERACEA;START SITES;MOUSE;DNA;TRANSCRIPTOME;PROTEIN;L.

期刊名称：PLANT MOLECULAR BIOLOGY （ 影响因子：4.076； 五年影响因子：4.89 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： 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.

分类号： Q946

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