Isolation and annotation of 10828 putative full length cDNAs from indica rice
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rice XIE Kabin(1) ZHANG Jianwei(1) XIANG Yong(1) FENG Qi(2) HAN Bin(2) CHU Zhaohui(1) WANG Shiping(1) ZHANG Qifa(1) XIONG Lizhong(1) 1. National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China 2. National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200233, China Science in China Series C-Life Sciences 2005 Vol.48 No. 5 pp.445-451 Code:062004-90 DOI:10.1360/062004-90 Abstract: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. KeywordsOryza sativa L., indica, functional genomics.