This Article Full Text Full Text (PDF) All Versions of this Article: 1532103v1 13/12/2725    most recent Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Vettore, A. L. Articles by Arruda, P. Search for Related Content PubMed PubMed Citation Articles by Vettore, A. L. Articles by Arruda, P. Social Bookmarking                   What's this?

Resources

Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane

¹ Centro de Biologia Molecular e Engenharia Genética, Instituto da Computação, Universidade Estadual de Campinas, 13083-970, Campinas–SP, Brazil ² Laboratório de Bioinformática, Instituto da Computação, Universidade Estadual de Campinas, 13083-970, Campinas–SP, Brazil ³ Departamento de Bioquímica, Instituto de Química, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900, São Paulo–SP, Brazil ⁴ Departamento de Botânica, Instituto de Biociências, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900, São Paulo–SP, Brazil ⁵ Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900, São Paulo–SP, Brazil ⁶ Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista, 14884-900, Jaboticabal–SP, Brazil ⁷ Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista, 14884-900, Jaboticabal–SP, Brazil ⁸ Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565–905 São Carlos–SP, Brazil ⁹ Departamento de Biotecnologia Vegetal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, 13600-970, Araras–SP, Brazil ¹⁰ Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900, Piracicaba–SP, Brazil ¹¹ Laboratório de Genética Molecular e Genomas, Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, 12244-000, São José dos Campos–SP, Brazil ¹² Departamento de Biotecnologia de Plantas Medicinais, Universidade de Ribeirão Preto, 14096-380, Ribeirão Preto–SP, Brazil ¹³ Centro de Estudos de Insetos Sociais, Instituto de Biociências, Universidade Estadual Paulista, 13506-900, Rio Claro–SP, Brazil ¹⁴ Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto–SP, Brazil ¹⁵ Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, 08780-911, Mogi das Cruzes–SP, Brazil ¹⁶ Centro de Genética, Biologia Molecular e Fitoquímica, Instituto Agronômico de Campinas, Caixa Postal 28, 13001-970, Campinas–SP, Brazil ¹⁷ Instituto de Física de São Carlos, Universidade de São Paulo, 13560-970, São Carlos–SP, Brazil ¹⁸ Departamento de Defesa Fitossanitária, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, 18603-970, Botucatu–SP, Brazil ¹⁹ Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista, 18618-000, Botucatu–SP, Brazil ²⁰ Centro APTA de Citros Sylvio Moreira, Instituto Agronômico de Campinas, 13490-970, Cordeiropolis–SP, Brazil ²¹ Departamento de Fonoaudiologia, Universidade Estadual Paulista, 17525-900, Marília–SP, Brazil ²² Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903, Ribeirão Preto–SP, Brazil ²³ CIRAD, TA 40/03, UMR 1096, 34398 Montpellier cedex 5, France

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.

²⁴ Present address: Instituto Ludwig de Pesquisa sobre o Câncer, 01509-010, São Paulo–SP, Brazil.

²⁵ Present address: Embrapa Recursos Genéticos e Biotecnologia–CENARGEN, Caixa Postal 02372, 70770-900, Brasilia–DF, Brazil.

²⁶ Present address: Monsanto Company, Mailzone Q4B, St. Louis, MO 63167, USA.

²⁷ Present address: Alellyx Applied Genomics, Rodovia Anhanguera, Km 104 (Techno Park), Rua James Clerk Maxwell, 320, 13067-850, Campinas–SP, Brazil.

²⁸ Present address: Scylla Bioinformatics, 13083-970, Campinas–SP, Brazil.

²⁹ Corresponding author.
E-MAIL parruda{at}unicamp.br; FAX (55-19) 3788 1089.

[Supplemental material is available online at http://sucest.lad.ic.unicamp.br/public. The sugarcane EST sequence data described in this paper have been submitted to GenBank under accession nos. CA064599–CA301538.]

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				J. Borecky, F. T. S. Nogueira, K. A. P. de Oliveira, I. G. Maia, A. E. Vercesi, and P. Arruda The plant energy-dissipating mitochondrial systems: depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots J. Exp. Bot., March 1, 2006; 57(4): 849 - 864. [Abstract] [Full Text] [PDF]

				J. A. Udall, J. M. Swanson, K. Haller, R. A. Rapp, M. E. Sparks, J. Hatfield, Y. Yu, Y. Wu, C. Dowd, A. B. Arpat, et al. A global assembly of cotton ESTs Genome Res., March 1, 2006; 16(3): 441 - 450. [Abstract] [Full Text] [PDF]

				A. H. Paterson, M. Freeling, and T. Sasaki Grains of knowledge: Genomics of model cereals Genome Res., December 1, 2005; 15(12): 1643 - 1650. [Abstract] [Full Text] [PDF]

				K. Kawaura, K. Mochida, and Y. Ogihara Expression Profile of Two Storage-Protein Gene Families in Hexaploid Wheat Revealed by Large-Scale Analysis of Expressed Sequence Tags Plant Physiology, December 1, 2005; 139(4): 1870 - 1880. [Abstract] [Full Text] [PDF]

				L. H. Pratt, C. Liang, M. Shah, F. Sun, H. Wang, St. P. Reid, A. R. Gingle, A. H. Paterson, R. Wing, R. Dean, et al. Sorghum Expressed Sequence Tags Identify Signature Genes for Drought, Pathogenesis, and Skotomorphogenesis from a Milestone Set of 16,801 Unique Transcripts Plant Physiology, October 1, 2005; 139(2): 869 - 884. [Abstract] [Full Text] [PDF]

				M. Vincentz, F. A.A. Cara, V. K. Okura, F. R. da Silva, G. L. Pedrosa, A. S. Hemerly, A. N. Capella, M. Marins, P. C. Ferreira, S. C. Franca, et al. Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome Plant Physiology, March 1, 2004; 134(3): 951 - 959. [Abstract] [Full Text] [PDF]