Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida

Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S. Inouye, Kuan Yang, Edward J. Perkins, Youping Deng

Research output: Contribution to journalArticle

Abstract

Background: Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR. Results: A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363-EH672369 and EL515444-EL515580) were obtained from the raw clone sequences after cleaning. Clustering analysis yielded 2231 unique sequences including 448 contigs (from 1361 ESTs) and 1783 singletons. Comparative genomic analysis showed that 743 or 33% of the unique sequences shared high similarity with existing genes in the GenBank nr database. Provisional function annotation assigned 830 Gene Ontology terms to 517 unique sequences based on their homology with the annotated genomes of four model organisms Drosophila melanogaster, Mus musculus, Saccharomyces cerevisiae, and Caenorhabditis elegans. Seven percent of the unique sequences were further mapped to 99 Kyoto Encyclopedia of Genes and Genomes pathways based on their matching Enzyme Commission numbers. All the information is stored and retrievable at a highly performed, web-based and user-friendly relational database called EST model database or ESTMD version 2. Conclusion: The ESTMD containing the sequence and annotation information of 4032 E. fetida ESTs is publicly accessible at http://mcbc.usm.edu/ estmd/.

Original languageEnglish (US)
Article numberS7
JournalBMC Bioinformatics
Volume8
Issue numberSUPPL. 7
DOIs
StatePublished - Nov 1 2007
Externally publishedYes

Fingerprint

Oligochaeta
Cloning
Expressed Sequence Tags
Annotation
Organism Cloning
Genes
Nucleic Acid Databases
Genome
Databases
Annelida
Ecotoxicology
Encyclopedias
Gene Ontology
Caenorhabditis elegans
Drosophila melanogaster
Ordnance
Libraries
Cluster Analysis
Saccharomyces cerevisiae
Gene

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

Pirooznia, M., Gong, P., Guan, X., Inouye, L. S., Yang, K., Perkins, E. J., & Deng, Y. (2007). Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida. BMC Bioinformatics, 8(SUPPL. 7), [S7]. https://doi.org/10.1186/1471-2105-8-S7-S7

Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida. / Pirooznia, Mehdi; Gong, Ping; Guan, Xin; Inouye, Laura S.; Yang, Kuan; Perkins, Edward J.; Deng, Youping.

In: BMC Bioinformatics, Vol. 8, No. SUPPL. 7, S7, 01.11.2007.

Research output: Contribution to journalArticle

Pirooznia, M, Gong, P, Guan, X, Inouye, LS, Yang, K, Perkins, EJ & Deng, Y 2007, 'Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida', BMC Bioinformatics, vol. 8, no. SUPPL. 7, S7. https://doi.org/10.1186/1471-2105-8-S7-S7
Pirooznia, Mehdi ; Gong, Ping ; Guan, Xin ; Inouye, Laura S. ; Yang, Kuan ; Perkins, Edward J. ; Deng, Youping. / Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida. In: BMC Bioinformatics. 2007 ; Vol. 8, No. SUPPL. 7.
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AB - Background: Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR. Results: A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363-EH672369 and EL515444-EL515580) were obtained from the raw clone sequences after cleaning. Clustering analysis yielded 2231 unique sequences including 448 contigs (from 1361 ESTs) and 1783 singletons. Comparative genomic analysis showed that 743 or 33% of the unique sequences shared high similarity with existing genes in the GenBank nr database. Provisional function annotation assigned 830 Gene Ontology terms to 517 unique sequences based on their homology with the annotated genomes of four model organisms Drosophila melanogaster, Mus musculus, Saccharomyces cerevisiae, and Caenorhabditis elegans. Seven percent of the unique sequences were further mapped to 99 Kyoto Encyclopedia of Genes and Genomes pathways based on their matching Enzyme Commission numbers. All the information is stored and retrievable at a highly performed, web-based and user-friendly relational database called EST model database or ESTMD version 2. Conclusion: The ESTMD containing the sequence and annotation information of 4032 E. fetida ESTs is publicly accessible at http://mcbc.usm.edu/ estmd/.

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