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

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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
License	This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.