title: Isolation and annotation of 10828 putative full length cDNAs from indica rice.
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.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Wuhan, Huazhong Agricultural University, Wuhan 430070, China
authors.forename: Kabin
authors.initials: K
authors.lastname: Xie
authors.forename: Jianwei
authors.initials: J
authors.lastname: Zhang
authors.forename: Yong
authors.initials: Y
authors.lastname: Xiang
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.forename: Bin
authors.initials: B
authors.lastname: Han
authors.forename: Zhaohui
authors.initials: Z
authors.lastname: Chu
authors.forename: Shiping
authors.initials: S
authors.lastname: Wang
authors.forename: Qifa
authors.initials: Q
authors.lastname: Zhang
authors.forename: Lizhong
authors.initials: L
authors.lastname: Xiong
mesh_terms: D018076:DNA, Complementary / Q000302:isolation & purification*; D015723:Gene Library; D012275:Oryza / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018076:DNA, Complementary