Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane
Autor(a) principal: | |
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Data de Publicação: | 2003 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1101/gr.1532103 http://hdl.handle.net/11449/10697 |
Resumo: | 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. |
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Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcaneTo 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.CIRAD, UMR 1096, F-34398 Montpellier 5, FranceUniv São Paulo, Fac Ciências Farmaceut Ribeirao Preto, Dept Ciências Farmaceut, BR-14040903 Ribeirao Preto, SP, BrazilUniv Estadual Paulista, Dept Fonoaudiol, BR-17525900 Marilia, SP, BrazilInst Agron Campinas, Ctr APTA Citros Sylvio Moreira, BR-13490970 Cordeiropolis, SP, BrazilUniv Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618000 Botucatu, SP, BrazilUniv Estadual Paulista, Fac Ciências Agron, Dept Defesa Fitossanitaria, BR-18603970 Botucatu, SP, BrazilUniv São Paulo, Inst Fis Sao Carlos, BR-13560970 Sao Carlos, SP, BrazilInst Agron Campinas, Ctr Genet Biol Mol & Fitoquim, BR-13001970 Campinas, SP, BrazilUniv Mogi das Cruzes, Nucleo Integrado Biotecnol, BR-08780911 Mogi Das Cruzes, SP, BrazilUniv São Paulo, Fac Filosofia Ciências & Letras Ribeirao Preto, Dept Biol, BR-14040901 Ribeirao Preto, SP, BrazilUniv Estadual Paulista, Inst Biociencias, Ctr Estudos Insetos Socias, BR-13506900 Rio Claro, SP, BrazilUniv Ribeirao Preto, Dept Biotecnol Plantas Med, BR-14096380 Ribeirao Preto, BrazilUniv Vale Paraiba, Inst Pesquisa & Desenvolvimento, Lab Genet Mol & Genomas, BR-12244000 Sao Jose Dos Campos, SP, BrazilUniv São Paulo, Escoal Super Agr Luiz de Queiroz, BR-13418900 Piracicaba, SP, BrazilUniv Fed Sao Carlos, Ctr Ciências Agrarias, Dept Biotecnol Vegetal, BR-13600970 Araras, SP, BrazilUniv Fed Sao Carlos, Dept Genet & Evolucao, BR-13565905 Sao Carlos, SP, BrazilUniv Estadual Paulista, Fac Ciências Agrarias & Vet Jaboticabal, Dept Biol Aplicada Agropecuaria, BR-14884900 Jaboticabal, SP, BrazilUniv Estadual Paulista, Fac Ciências Agrarias & Vet Jaboticabal, Dept Tecnol, BR-14884900 Jaboticabal, SP, BrazilUniv São Paulo, Inst Ciências Biomed, Dept Microbiol, BR-05508900 São Paulo, BrazilUniv São Paulo, Inst Biociencias, Dept Bot, BR-05508900 São Paulo, BrazilUniv São Paulo, Inst Quim, Dept Bioquim, BR-05508900 São Paulo, BrazilUniv Estadual Campinas, Inst Computacao, Lab Bioinformat, BR-13083970 Campinas, SP, BrazilUniv Estadual Campinas, Ctr Biol Mol & Engn Genet, BR-13083970 Campinas, SP, BrazilUniv Estadual Paulista, Dept Fonoaudiol, BR-17525900 Marilia, SP, BrazilUniv Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618000 Botucatu, SP, BrazilUniv Estadual Paulista, Fac Ciências Agron, Dept Defesa Fitossanitaria, BR-18603970 Botucatu, SP, BrazilUniv Estadual Paulista, Inst Biociencias, Ctr Estudos Insetos Socias, BR-13506900 Rio Claro, SP, BrazilUniv Estadual Paulista, Fac Ciências Agrarias & Vet Jaboticabal, Dept Biol Aplicada Agropecuaria, BR-14884900 Jaboticabal, SP, BrazilUniv Estadual Paulista, Fac Ciências Agrarias & Vet Jaboticabal, Dept Tecnol, BR-14884900 Jaboticabal, SP, BrazilCold Spring Harbor Lab Press, Publications DeptCIRADUniversidade de São Paulo (USP)Universidade Estadual Paulista (Unesp)Inst Agron CampinasUniv Mogi das CruzesUniv Ribeirao PretoUniv Vale ParaibaUniversidade Federal de São Carlos (UFSCar)Universidade Estadual de Campinas (UNICAMP)Vettore, A. L.da Silva, F. R.Kemper, E. L.Souza, G. M.da Silva, A. M.Ferro, MITHenrique-Silva, F.Giglioti, E. A.Lemos, MVFCoutinho, L. L.Nobrega, M. P.Carrer, H.Franca, S. C.Bacci, M.Goldman, MHSGomes, S. L.Nunes, L. R.Camargo, LEASiqueira, W. J.Van Sluys, M. A.Thiemann, O. H.Kuramae, E. E.Santelli, R. V.Marino, C. L.Targon, MLPNFerro, J. A.Silveira, HCSMarini, D. C.Lemos, EGMMonteiro-Vitorello, C. B.Tambor, JHMCarraro, D. M.Roberto, P. G.Martins, V. G.Goldman, G. H.de Oliveira, R. C.Truffi, D.Colombo, C. A.Rossi, M.de Araujo, P. G.Sculaccio, S. A.Angella, A.Lima, MMAde Rosa, V. E.Siviero, F.Coscrato, V. E.Machado, M. A.Grivet, L.Di Mauro, SMZNobrega, F. G.Menck, CFMBraga, MDVTelles, G. P.Cara, FAAPedrosa, G.Meidanis, J.Arruda, P.2014-05-20T13:31:25Z2014-05-20T13:31:25Z2003-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article2725-2735application/pdfhttp://dx.doi.org/10.1101/gr.1532103Genome Research. Cold Spring Harbor: Cold Spring Harbor Lab Press, Publications Dept, v. 13, n. 12, p. 2725-2735, 2003.1088-9051http://hdl.handle.net/11449/1069710.1101/gr.1532103WOS:000186920200023WOS000186920200023.pdf01653487382083190000-0003-4524-954XWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGenome Research10.10112,367info:eu-repo/semantics/openAccess2024-04-30T18:07:55Zoai:repositorio.unesp.br:11449/10697Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-04-30T18:07:55Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane |
title |
Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane |
spellingShingle |
Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane Vettore, A. L. |
title_short |
Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane |
title_full |
Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane |
title_fullStr |
Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane |
title_full_unstemmed |
Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane |
title_sort |
Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane |
author |
Vettore, A. L. |
author_facet |
Vettore, A. L. da Silva, F. R. Kemper, E. L. Souza, G. M. da Silva, A. M. Ferro, MIT Henrique-Silva, F. Giglioti, E. A. Lemos, MVF Coutinho, L. L. Nobrega, M. P. Carrer, H. Franca, S. C. Bacci, M. Goldman, MHS Gomes, S. L. Nunes, L. R. Camargo, LEA Siqueira, W. J. Van Sluys, M. A. Thiemann, O. H. Kuramae, E. E. Santelli, R. V. Marino, C. L. Targon, MLPN Ferro, J. A. Silveira, HCS Marini, D. C. Lemos, EGM Monteiro-Vitorello, C. B. Tambor, JHM Carraro, D. M. Roberto, P. G. Martins, V. G. Goldman, G. H. de Oliveira, R. C. Truffi, D. Colombo, C. A. Rossi, M. de Araujo, P. G. Sculaccio, S. A. Angella, A. Lima, MMA de Rosa, V. E. Siviero, F. Coscrato, V. E. Machado, M. A. Grivet, L. Di Mauro, SMZ Nobrega, F. G. Menck, CFM Braga, MDV Telles, G. P. Cara, FAA Pedrosa, G. Meidanis, J. Arruda, P. |
author_role |
author |
author2 |
da Silva, F. R. Kemper, E. L. Souza, G. M. da Silva, A. M. Ferro, MIT Henrique-Silva, F. Giglioti, E. A. Lemos, MVF Coutinho, L. L. Nobrega, M. P. Carrer, H. Franca, S. C. Bacci, M. Goldman, MHS Gomes, S. L. Nunes, L. R. Camargo, LEA Siqueira, W. J. Van Sluys, M. A. Thiemann, O. H. Kuramae, E. E. Santelli, R. V. Marino, C. L. Targon, MLPN Ferro, J. A. Silveira, HCS Marini, D. C. Lemos, EGM Monteiro-Vitorello, C. B. Tambor, JHM Carraro, D. M. Roberto, P. G. Martins, V. G. Goldman, G. H. de Oliveira, R. C. Truffi, D. Colombo, C. A. Rossi, M. de Araujo, P. G. Sculaccio, S. A. Angella, A. Lima, MMA de Rosa, V. E. Siviero, F. Coscrato, V. E. Machado, M. A. Grivet, L. Di Mauro, SMZ Nobrega, F. G. Menck, CFM Braga, MDV Telles, G. P. Cara, FAA Pedrosa, G. Meidanis, J. Arruda, P. |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
CIRAD Universidade de São Paulo (USP) Universidade Estadual Paulista (Unesp) Inst Agron Campinas Univ Mogi das Cruzes Univ Ribeirao Preto Univ Vale Paraiba Universidade Federal de São Carlos (UFSCar) Universidade Estadual de Campinas (UNICAMP) |
dc.contributor.author.fl_str_mv |
Vettore, A. L. da Silva, F. R. Kemper, E. L. Souza, G. M. da Silva, A. M. Ferro, MIT Henrique-Silva, F. Giglioti, E. A. Lemos, MVF Coutinho, L. L. Nobrega, M. P. Carrer, H. Franca, S. C. Bacci, M. Goldman, MHS Gomes, S. L. Nunes, L. R. Camargo, LEA Siqueira, W. J. Van Sluys, M. A. Thiemann, O. H. Kuramae, E. E. Santelli, R. V. Marino, C. L. Targon, MLPN Ferro, J. A. Silveira, HCS Marini, D. C. Lemos, EGM Monteiro-Vitorello, C. B. Tambor, JHM Carraro, D. M. Roberto, P. G. Martins, V. G. Goldman, G. H. de Oliveira, R. C. Truffi, D. Colombo, C. A. Rossi, M. de Araujo, P. G. Sculaccio, S. A. Angella, A. Lima, MMA de Rosa, V. E. Siviero, F. Coscrato, V. E. Machado, M. A. Grivet, L. Di Mauro, SMZ Nobrega, F. G. Menck, CFM Braga, MDV Telles, G. P. Cara, FAA Pedrosa, G. Meidanis, J. Arruda, P. |
description |
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. |
publishDate |
2003 |
dc.date.none.fl_str_mv |
2003-12-01 2014-05-20T13:31:25Z 2014-05-20T13:31:25Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1101/gr.1532103 Genome Research. Cold Spring Harbor: Cold Spring Harbor Lab Press, Publications Dept, v. 13, n. 12, p. 2725-2735, 2003. 1088-9051 http://hdl.handle.net/11449/10697 10.1101/gr.1532103 WOS:000186920200023 WOS000186920200023.pdf 0165348738208319 0000-0003-4524-954X |
url |
http://dx.doi.org/10.1101/gr.1532103 http://hdl.handle.net/11449/10697 |
identifier_str_mv |
Genome Research. Cold Spring Harbor: Cold Spring Harbor Lab Press, Publications Dept, v. 13, n. 12, p. 2725-2735, 2003. 1088-9051 10.1101/gr.1532103 WOS:000186920200023 WOS000186920200023.pdf 0165348738208319 0000-0003-4524-954X |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Genome Research 10.101 12,367 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
2725-2735 application/pdf |
dc.publisher.none.fl_str_mv |
Cold Spring Harbor Lab Press, Publications Dept |
publisher.none.fl_str_mv |
Cold Spring Harbor Lab Press, Publications Dept |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1799965653040365568 |