Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane

作者：Vettore AL; da Silva FR; Kemper EL; Souza GM; da Silva AM; Ferro MIT; Henrique Silva F; Giglioti EA; Lemos MVF; Coutinho LL; Nobrega MP; Carrer H; Franca SC; Bacci M; Goldman MHS; Gomes SL; Nunes LR; Camargo LEA; Siqueira WJ; Van Sluys MA; Thiemann OH; Kuramae EE; Santelli RV; Marino CL; Targon MLPN; Ferro JA; Silveira HCS; Marini DC; Lemos EGM; Monteiro Vitorello CB; Tambor JHM; Carraro DM; Roberto PG; Martins VG; Goldman GH; de Oliveira RC; Truffi D

来源：Genome Research, 2003, 13(12): 2725-2735.

DOI：10.1101/gr.1532103

To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST),program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.

• 出版日期2003-12