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

André L. Vettore; Felipe R. da Silva; Edson L. Kemper; Glaucia M. Souza; Aline M. da Silva; Maria Inês T. Ferro; Flavio Henrique-Silva; Éder A. Giglioti; Manoel V.F. Lemos; Luiz L. Coutinho; Marina P. Nobrega; Helaine Carrer; Suzelei C. França; Maurício Bacci; Maria Helena S. Goldman; Suely L. Gomes; Luiz R. Nunes; Luis E.A. Camargo; Walter J. Siqueira; Marie Anne Van Sluys; Otavio H. Thiemann; Eiko E. Kuramae; Roberto V. Santelli; Celso L. Marino; Maria L.P.N. Targon; Jesus A. Ferro; Henrique C.S. Silveira; Danyelle C. Marini; Eliana G.M. Lemos; Claudia B. Monteiro-Vitorello; José H.M. Tambor; Dirce M. Carraro; Patrícia G. Roberto; Vanderlei G. Martins; Gustavo H. Goldman; Regina C. de Oliveira; Daniela Truffi; Carlos A. Colombo; Magdalena Rossi; Paula G. de Araujo; Susana A. Sculaccio; Aline Angella; Marleide M.A. Lima; Vicente E. de Rosa; Fábio Siviero; Virginia E. Coscrato; Marcos A. Machado; Laurent Grivet; Sonia M.Z. Di Mauro; Francisco G. Nobrega; Carlos F.M. Menck; Marilia D.V. Braga; Guilherme P. Telles; Frank A.A. Cara; Guilherme Pedrosa; João Meidanis; Paulo Arruda

doi:10.1101/gr.1532103

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

André L. Vettore, Felipe R. da Silva, Edson L. Kemper, Glaucia M. Souza, Aline M. da Silva, Maria Inês T. Ferro, Flavio Henrique-Silva, Éder A. Giglioti, Manoel V.F. Lemos, Luiz L. Coutinho, Marina P. Nobrega, Helaine Carrer, Suzelei C. França, Maurício Bacci, Maria Helena S. Goldman, Suely L. Gomes, Luiz R. Nunes, Luis E.A. Camargo, Walter J. Siqueira, Marie Anne Van SluysOtavio H. Thiemann, Eiko E. Kuramae, Roberto V. Santelli, Celso L. Marino, Maria L.P.N. Targon, Jesus A. Ferro, Henrique C.S. Silveira, Danyelle C. Marini, Eliana G.M. Lemos, Claudia B. Monteiro-Vitorello, José H.M. Tambor, Dirce M. Carraro, Patrícia G. Roberto, Vanderlei G. Martins, Gustavo H. Goldman, Regina C. de Oliveira, Daniela Truffi, Carlos A. Colombo, Magdalena Rossi, Paula G. de Araujo, Susana A. Sculaccio, Aline Angella, Marleide M.A. Lima, Vicente E. de Rosa, Fábio Siviero, Virginia E. Coscrato, Marcos A. Machado, Laurent Grivet, Sonia M.Z. Di Mauro, Francisco G. Nobrega, Carlos F.M. Menck, Marilia D.V. Braga, Guilherme P. Telles, Frank A.A. Cara, Guilherme Pedrosa, João Meidanis, Paulo Arruda^*

^*Bijbehorende auteur voor dit werk

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

238 Citaten (Scopus)

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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.

Originele taal-2	Engels
Pagina's (van-tot)	2725-2735
Aantal pagina's	11
Tijdschrift	Genome Research
Volume	13
Nummer van het tijdschrift	12
DOI's	https://doi.org/10.1101/gr.1532103
Status	Gepubliceerd - dec. 2003

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Vettore, A. L., da Silva, F. R., Kemper, E. L., Souza, G. M., da Silva, A. M., Ferro, M. I. T., Henrique-Silva, F., Giglioti, É. A., Lemos, M. V. F., Coutinho, L. L., Nobrega, M. P., Carrer, H., França, S. C., Bacci, M., Goldman, M. H. S., Gomes, S. L., Nunes, L. R., Camargo, L. E. A., Siqueira, W. J., ... Arruda, P. (2003). Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Research, 13(12), 2725-2735. https://doi.org/10.1101/gr.1532103

@article{21bd54d4a96a4d24a587023eba6d8b73,

title = "Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane",

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.",

author = "Vettore, {Andr{\'e} L.} and {da Silva}, {Felipe R.} and Kemper, {Edson L.} and Souza, {Glaucia M.} and {da Silva}, {Aline M.} and Ferro, {Maria In{\^e}s T.} and Flavio Henrique-Silva and Giglioti, {{\'E}der A.} and Lemos, {Manoel V.F.} and Coutinho, {Luiz L.} and Nobrega, {Marina P.} and Helaine Carrer and Fran{\c c}a, {Suzelei C.} and Maur{\'i}cio Bacci and Goldman, {Maria Helena S.} and Gomes, {Suely L.} and Nunes, {Luiz R.} and Camargo, {Luis E.A.} and Siqueira, {Walter J.} and {Van Sluys}, {Marie Anne} and Thiemann, {Otavio H.} and Kuramae, {Eiko E.} and Santelli, {Roberto V.} and Marino, {Celso L.} and Targon, {Maria L.P.N.} and Ferro, {Jesus A.} and Silveira, {Henrique C.S.} and Marini, {Danyelle C.} and Lemos, {Eliana G.M.} and Monteiro-Vitorello, {Claudia B.} and Tambor, {Jos{\'e} H.M.} and Carraro, {Dirce M.} and Roberto, {Patr{\'i}cia G.} and Martins, {Vanderlei G.} and Goldman, {Gustavo H.} and {de Oliveira}, {Regina C.} and Daniela Truffi and Colombo, {Carlos A.} and Magdalena Rossi and {de Araujo}, {Paula G.} and Sculaccio, {Susana A.} and Aline Angella and Lima, {Marleide M.A.} and {de Rosa}, {Vicente E.} and F{\'a}bio Siviero and Coscrato, {Virginia E.} and Machado, {Marcos A.} and Laurent Grivet and {Di Mauro}, {Sonia M.Z.} and Nobrega, {Francisco G.} and Menck, {Carlos F.M.} and Braga, {Marilia D.V.} and Telles, {Guilherme P.} and Cara, {Frank A.A.} and Guilherme Pedrosa and Jo{\~a}o Meidanis and Paulo Arruda",

year = "2003",

month = dec,

doi = "10.1101/gr.1532103",

language = "English",

volume = "13",

pages = "2725--2735",

journal = "Genome Research",

issn = "1088-9051",

publisher = "Cold Spring Harbor Laboratory Press",

number = "12",

}

Vettore, AL, da Silva, FR, Kemper, EL, Souza, GM, da Silva, AM, Ferro, MIT, Henrique-Silva, F, Giglioti, ÉA, Lemos, MVF, Coutinho, LL, Nobrega, MP, Carrer, H, França, 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 2003, 'Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane', Genome Research, vol. 13, nr. 12, blz. 2725-2735. https://doi.org/10.1101/gr.1532103

TY - JOUR

T1 - Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane

AU - Vettore, André L.

AU - da Silva, Felipe R.

AU - Kemper, Edson L.

AU - Souza, Glaucia M.

AU - da Silva, Aline M.

AU - Ferro, Maria Inês T.

AU - Henrique-Silva, Flavio

AU - Giglioti, Éder A.

AU - Lemos, Manoel V.F.

AU - Coutinho, Luiz L.

AU - Nobrega, Marina P.

AU - Carrer, Helaine

AU - França, Suzelei C.

AU - Bacci, Maurício

AU - Goldman, Maria Helena S.

AU - Gomes, Suely L.

AU - Nunes, Luiz R.

AU - Camargo, Luis E.A.

AU - Siqueira, Walter J.

AU - Van Sluys, Marie Anne

AU - Thiemann, Otavio H.

AU - Kuramae, Eiko E.

AU - Santelli, Roberto V.

AU - Marino, Celso L.

AU - Targon, Maria L.P.N.

AU - Ferro, Jesus A.

AU - Silveira, Henrique C.S.

AU - Marini, Danyelle C.

AU - Lemos, Eliana G.M.

AU - Monteiro-Vitorello, Claudia B.

AU - Tambor, José H.M.

AU - Carraro, Dirce M.

AU - Roberto, Patrícia G.

AU - Martins, Vanderlei G.

AU - Goldman, Gustavo H.

AU - de Oliveira, Regina C.

AU - Truffi, Daniela

AU - Colombo, Carlos A.

AU - Rossi, Magdalena

AU - de Araujo, Paula G.

AU - Sculaccio, Susana A.

AU - Angella, Aline

AU - Lima, Marleide M.A.

AU - de Rosa, Vicente E.

AU - Siviero, Fábio

AU - Coscrato, Virginia E.

AU - Machado, Marcos A.

AU - Grivet, Laurent

AU - Di Mauro, Sonia M.Z.

AU - Nobrega, Francisco G.

AU - Menck, Carlos F.M.

AU - Braga, Marilia D.V.

AU - Telles, Guilherme P.

AU - Cara, Frank A.A.

AU - Pedrosa, Guilherme

AU - Meidanis, João

AU - Arruda, Paulo

PY - 2003/12

Y1 - 2003/12

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=10744219560&partnerID=8YFLogxK

U2 - 10.1101/gr.1532103

DO - 10.1101/gr.1532103

M3 - Article

C2 - 14613979

AN - SCOPUS:10744219560

SN - 1088-9051

VL - 13

SP - 2725

EP - 2735

JO - Genome Research

JF - Genome Research

IS - 12

ER -

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

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