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Open Access Database

Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome

Hyun-Jin Kim1, Kwang-Hyun Baek2, Seung-Won Lee1, JungEun Kim1, Bong-Woo Lee1, Hye-Sun Cho3, Woo Taek Kim4, Doil Choi5* and Cheol-Goo Hur1*

Author Affiliations

1 Omics Integration Research Center, KRIBB, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea

2 School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea

3 Plant Genome Research Center, KRIBB, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea

4 Department of Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea

5 Department of Plant Science, Seoul National University, Seoul 151-921, Korea

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BMC Plant Biology 2008, 8:101  doi:10.1186/1471-2229-8-101

Published: 9 October 2008

Abstract

Background

There is no dedicated database available for Expressed Sequence Tags (EST) of the chili pepper (Capsicum annuum), although the interest in a chili pepper EST database is increasing internationally due to the nutritional, economic, and pharmaceutical value of the plant. Recent advances in high-throughput sequencing of the ESTs of chili pepper cv. Bukang have produced hundreds of thousands of complementary DNA (cDNA) sequences. Therefore, a chili pepper EST database was designed and constructed to enable comprehensive analysis of chili pepper gene expression in response to biotic and abiotic stresses.

Results

We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO), and MIPS Functional Catalogue (FunCat). The Pepper EST database is designed to provide a workbench for (i) identifying unigenes in pepper plants, (ii) analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii) comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at http://genepool.kribb.re.kr/pepper/ webcite.

Conclusion

The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.