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

Author(s):  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, Colombo CA, Rossi M, de Araujo PG, Sculaccio SA, Angella A, Lima MMA, de Rosa VE, Siviero F, Coscrato VE, Machado MA, Grivet L, Di Mauro SMZ, Nobrega FG, Menck CFM, Braga MDV, Telles GP, Cara FAA, Pedrosa G, Meidanis J, Arruda P

Source:  GENOME RESEARCH 13 (12): 2725-2735 DEC 2003

Document Type:  Article

Language:  English

Abstract:  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.

KeyWords Plus:  SINGLE NUCLEOTIDE POLYMORPHISMS; CDNA MICROARRAYS; GENOME STRUCTURE; DRAFT SEQUENCE; EST DATA; GENES; SACCHARUM; ORGANIZATION; EVOLUTION; DATABASE

Addresses:  Arruda P (reprint author), Alellyx Appl Genomics, Rodovia Anhanguera Km 104,Techno Pk,Rua James Cle, Campinas, SP BR-13067850 Brazil
CIRAD, UMR 1096, Montpellier, F-34398 5 France
Univ Sao Paulo, Fac Ciencias Farmaceut Ribeirao Preto, Dept Ciencias Farmaceut, Ribeirao Preto, SP BR-14040903 Brazil
Univ Estadual Paulista, Dept Fonoaudiol, Marilia, SP BR-17525900 Brazil
Inst Agron Campinas, Ctr APTA Citros Sylvio Moreira, Cordeiropolis, SP BR-13490970 Brazil
Univ Estadual Paulista, Inst Biociencias, Dept Genet, Botucatu, SP BR-18618000 Brazil
Univ Estadual Paulista, Fac Ciencias Agron, Dept Defesa Fitossanitaria, Botucatu, SP BR-18603970 Brazil
Univ Sao Paulo, Inst Fis Sao Carlos, Sao Carlos, SP BR-13560970 Brazil
Inst Agron Campinas, Ctr Genet Biol Mol & Fitoquim, Campinas, SP BR-13001970 Brazil
Univ Mogi das Cruzes, Nucleo Integrado Biotecnol, Mogi Das Cruzes, SP BR-08780911 Brazil
Univ Sao Paulo, Fac Filosofia Ciencias & Letras Ribeirao Preto, Dept Biol, Ribeirao Preto, SP BR-14040901 Brazil
Univ Estadual Paulista, Inst Biociencias, Ctr Estudos Insetos Socias, Rio Claro, SP BR-13506900 Brazil
Univ Ribeirao Preto, Dept Biotecnol Plantas Med, Ribeirao Preto, BR-14096380 Brazil
Univ Vale Paraiba, Inst Pesquisa & Desenvolvimento, Lab Genet Mol & Genomas, Sao Jose Dos Campos, SP BR-12244000 Brazil
Univ Sao Paulo, Escoal Super Agr Luiz de Queiroz, Piracicaba, SP BR-13418900 Brazil
Univ Fed Sao Carlos, Ctr Ciencias Agrarias, Dept Biotecnol Vegetal, Araras, SP BR-13600970 Brazil
Univ Fed Sao Carlos, Dept Genet & Evolucao, Sao Carlos, SP BR-13565905 Brazil
Univ Estadual Paulista, Fac Ciencias Agrarias & Vet Jaboticabal, Dept Biol Aplicada Agropecuaria, Jaboticabal, SP BR-14884900 Brazil
Univ Estadual Paulista, Fac Ciencias Agrarias & Vet Jaboticabal, Dept Tecnol, Jaboticabal, SP BR-14884900 Brazil
Univ Sao Paulo, Inst Ciencias Biomed, Dept Microbiol, Sao Paulo, BR-05508900 Brazil
Univ Sao Paulo, Inst Biociencias, Dept Bot, Sao Paulo, BR-05508900 Brazil
Univ Sao Paulo, Inst Quim, Dept Bioquim, Sao Paulo, BR-05508900 Brazil
Univ Estadual Campinas, Inst Computacao, Lab Bioinformat, Campinas, SP BR-13083970 Brazil
Univ Estadual Campinas, Ctr Biol Mol & Engn Genet, Campinas, SP BR-13083970 Brazil

Publisher:  COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2924 USA

Subject Category:  BIOCHEMISTRY & MOLECULAR BIOLOGY; BIOTECHNOLOGY & APPLIED MICROBIOLOGY; GENETICS & HEREDITY

IDS Number:  749KZ

ISSN:  1088-9051