Isolation and annotation of 10828 putative full length cDNAs from indica rice.
We reported the isolation and identification of 10828 putative full-length cDNAs (FL-cDNA) from an indica rice cultivar, Minghui 63, with the long-term goal to isolate all full-length cDNAs from indica genome. Comparison with the databases showed that 780 of them are new rice cDNAs with no match in japonica cDNA database. Totally, 9078 of the FL-cDNAs contained predicted ORFs matching with japonica FL-cDNAs and 6543 could find homologous proteins with complete ORFs. 53% of the matched FL-cDNAs isolated in this study had longer 5'UTR than japonica FL-cDNAs. In silico mapping showed that 9776 (90.28%) of the FL-cDNAs had matched genomic sequences in the japonica genome and 10046 (92.78%) had matched genomic sequences in the indica genome. The average nucleotide sequence identity between the two subspecies is 99.2%. A majority of FL-cDNAs (90%) could be classified with GO (gene ontology) terms based on homology proteins. More than 60% of the new cDNAs isolated in this study had no homology to the known proteins. This set of FL-cDNAs should be useful for functional genomics and proteomics studies.
Xie
Kabin
K
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Wuhan, Huazhong Agricultural University, Wuhan 430070, China
Zhang
Jianwei
J
Xiang
Yong
Y
Feng
Qi
Q
Han
Bin
B
Chu
Zhaohui
Z
Wang
Shiping
S
Zhang
Qifa
Q
Xiong
Lizhong
L
D018076:DNA, Complementary / Q000302:isolation & purification*; D015723:Gene Library; D012275:Oryza / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity
D018076:DNA, Complementary