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Title

The capsicum transcriptome DB: a "hot" tool for genomic research

 

Authors

Elsa Góngora-Castillo1, Rubén Fajardo-Jaime3, Araceli Fernández-Cortes2, Alba E. Jofre- Garfias1, Edmundo Lozoya-Gloria1, Octavio Martínez2, Neftalí Ochoa-Alejo1, Rafael Rivera-Bustamante1*

 

Affiliation

1Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del I.P.N (Cinvestav)-Unidad Irapuato, Km 9.6 Libramiento Norte, Carretera Irapuato-León, 36821-Irapuato, Gto., México; 2 Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Cinvestav-Irapuato, Km 9.6 Libramiento Norte, carretera Irapuato-León, 36821-Irapuato, Gto., México; 3 División de Ciencias Económicas y Administrativas, Universidad de Guanajuato, Fracc. El Establo. Campus Guanajuato. 36250. Guanajuato, Gto., México

 

Email

rrivera@ira.cinvestav.mx; *Corresponding author

 

Article Type

Database

 

Date

Received November 14, 2011; Accepted December 17, 2011; Pubished January 06, 2012

 

Abstract

Chili pepper (Capsicum annuum) is an economically important crop with no available public genome sequence. We describe a genomic resource to facilitate Capsicum annuum research. A collection of Expressed Sequence Tags (ESTs) derived from five C. annuum organs (root, stem, leaf, flower and fruit) were sequenced using the Sanger method and multiple leaf transcriptomes were deeply sampled using with GS-pyrosequencing. A hybrid assembly of 1,324,516 raw reads yielded 32,314 high quality contigs as validated by coverage and identity analysis with existing pepper sequences. Overall, 75.5% of the contigs had significant sequence similarity to entries in nucleic acid and protein databases; 23% of the sequences have not been previously reported for C. annuum and expand sequence resources for this species. A MySQL database and a user-friendly Web interface were constructed with search-tools that permit queries of the ESTs including sequence, functional annotation, Gene Ontology classification, metabolic pathways, and assembly information. The Capsicum Transcriptome DB is free available from http://www.bioingenios.ira.cinvestav.mx:81/Joomla/

 

Citation

Góngora-Castillo et al. Bioinformation 8(1): 043-047 (2012)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

Copyright

Publisher

 

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

 

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.