Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus
- Equal contributors
1 Cardiff School of Biosciences, BIOSI 1, University of Cardiff, P.O. Box 915, Cardiff, CF10 3TL, UK
2 Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3JT, UK
3 Centre for Ecology and Hydrology, Monks Wood, Abbots Ripton, Huntingdon, Cambridgeshire, PE28 2LS, UK
4 Microarray Department and Integrative Bioinformatics Unit, Faculty of Science, University of Amsterdam, Kruislaan 318, Building I, Room 105C, 1098 SM Amsterdam, The Netherlands
5 School of Biomedical and Health Sciences, Pharmaceutical Sciences Division, Franklin Wilkins Building 150, Stamford St., London, SE1 9NH, UK
BMC Genomics 2008, 9:266 doi:10.1186/1471-2164-9-266Published: 3 June 2008
Natural contamination and anthropogenic pollution of soils are likely to be major determinants of functioning and survival of keystone invertebrate taxa. Soil animals will have both evolutionary adaptation and genetically programmed responses to these toxic chemicals, but mechanistic understanding of such is sparse. The clitellate annelid Lumbricus rubellus is a model organism for soil health testing, but genetic data have been lacking.
We generated a 17,000 sequence expressed sequence tag dataset, defining ~8,100 different putative genes, and built an 8,000-element transcriptome microarray for L. rubellus. Strikingly, less than half the putative genes (43%) were assigned annotations from the gene ontology (GO) system; this reflects the phylogenetic uniqueness of earthworms compared to the well-annotated model animals. The microarray was used to identify adult- and juvenile-specific transcript profiles in untreated animals and to determine dose-response transcription profiles following exposure to three xenobiotics from different chemical classes: inorganic (the metal cadmium), organic (the polycyclic aromatic hydrocarbon fluoranthene), and agrochemical (the herbicide atrazine). Analysis of these profiles revealed compound-specific fingerprints which identify the molecular responses of this annelid to each contaminant. The data and analyses are available in an integrated database, LumbriBASE.
L. rubellus has a complex response to contaminant exposure, but this can be efficiently analysed using molecular methods, revealing unique response profiles for different classes of effector. These profiles may assist in the development of novel monitoring or bioremediation protocols, as well as in understanding the ecosystem effects of exposure.