Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 357453
Title Collembase: a repository for springtail genomics and soil quality assessment
Author(s) Timmermans, M.J.T.N.; Boer, M.E. de; Nota, B.; Marien, J.; Klein Lankhorst, R.M.; Straalen, N.M. van; Roelofs, D.
Source BMC Genomics 8 (2007). - ISSN 1471-2164 - 10 p.
DOI https://doi.org/10.1186/1471-2164-8-341
Department(s) PRI Bioscience
Publication type Refereed Article in a scientific journal
Publication year 2007
Keyword(s) insect orchesella-cincta - gene-expression profiles - folsomia-candida - phylogenetic analysis - risk-assessment - ecotoxicology - toxicogenomics - toxicity - ecotoxicogenomics - hexapoda
Abstract Environmental quality assessment is traditionally based on responses of reproduction and survival of indicator organisms. For soil assessment the springtail Folsomia candida (Collembola) is an accepted standard test organism. We argue that environmental quality assessment using gene expression profiles of indicator organisms exposed to test substrates is more sensitive, more toxicant specific and significantly faster than current risk assessment methods. To apply this species as a genomic model for soil quality testing we conducted an EST sequencing project and developed an online database. Description: Collembase is a web-accessible database comprising springtail (F. candida) genomic data. Presently, the database contains information on 8686 ESTs that are assembled into 5952 unique gene objects. Of those gene objects ~40% showed homology to other protein sequences available in GenBank (blastx analysis; non-redundant (nr) database; expect-value <10-5). Software was applied to infer protein sequences. The putative peptides, which had an average length of 115 amino-acids (ranging between 23 and 440) were annotated with Gene Ontology (GO) terms. In total 1025 peptides (~17% of the gene objects) were assigned at least one GO term (expect-value <10-25). Within Collembase searches can be conducted based on BLAST and GO annotation, cluster name or using a BLAST server. The system furthermore enables easy sequence retrieval for functional genomic and Quantitative-PCR experiments. Sequences are submitted to GenBank (Accession numbers: EV473060 - EV481745). CONCLUSION: Collembase (http://www.collembase.org) is a resource of sequence data on the springtail F. candida. The information within the database will be linked to a custom made microarray, based on the Agilent platform, which can be applied for soil quality testing. In addition, Collembase supplies information that is valuable for related scientific disciplines such as molecular ecology, ecogenomics, molecular evolution and phylogenetics.
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