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

Hyun Jin Kim, Kwang Hyun Baek, Seung Won Lee, Jung Eun Kim, Bong Woo Lee, Hye Sun Cho, Woo Taek Kim, Doil Choi, Cheol Goo Hur

Research output: Contribution to journalArticle

42 Citations (Scopus)

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/. 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.

Original languageEnglish
Article number101
JournalBMC Plant Biology
Volume8
DOIs
Publication statusPublished - 2008 Nov 6

Fingerprint

hot peppers
sweet peppers
Capsicum annuum
expressed sequence tags
transcriptome
unigenes
complementary DNA
Solanaceae
plant diseases and disorders
biotic stress
abiotic stress
biochemical pathways
genes
nucleotide sequences
drugs
economics
gene expression
genome

All Science Journal Classification (ASJC) codes

  • Plant Science

Cite this

Kim, Hyun Jin ; Baek, Kwang Hyun ; Lee, Seung Won ; Kim, Jung Eun ; Lee, Bong Woo ; Cho, Hye Sun ; Kim, Woo Taek ; Choi, Doil ; Hur, Cheol Goo. / Pepper EST database : Comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome. In: BMC Plant Biology. 2008 ; Vol. 8.
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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/. 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.",
author = "Kim, {Hyun Jin} and Baek, {Kwang Hyun} and Lee, {Seung Won} and Kim, {Jung Eun} and Lee, {Bong Woo} and Cho, {Hye Sun} and Kim, {Woo Taek} and Doil Choi and Hur, {Cheol Goo}",
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Pepper EST database : Comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome. / Kim, Hyun Jin; Baek, Kwang Hyun; Lee, Seung Won; Kim, Jung Eun; Lee, Bong Woo; Cho, Hye Sun; Kim, Woo Taek; Choi, Doil; Hur, Cheol Goo.

In: BMC Plant Biology, Vol. 8, 101, 06.11.2008.

Research output: Contribution to journalArticle

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AU - Lee, Bong Woo

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N2 - 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/. 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.

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