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Edinburgh Research Explorer View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Edinburgh Research Explorer Edinburgh Research Explorer Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus Citation for published version: Owen, J, Hedley, BA, Svendsen, C, Wren, J, Jonker, MJ, Hankard, PK, Lister, LJ, Stürzenbaum, SR, Morgan, AJ, Spurgeon, DJ, Blaxter, ML & Kille, P 2008, 'Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus' BMC Genomics, vol. 9, no. 266, pp. -. DOI: 10.1186/1471-2164-9-266 Digital Object Identifier (DOI): 10.1186/1471-2164-9-266 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: BMC Genomics Publisher Rights Statement: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 05. Apr. 2019 BMC Genomics BioMed Central Research article Open Access Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus Jennifer Owen†1, B Ann Hedley†2, Claus Svendsen3, Jodie Wren1,3, Martijs J Jonker4, Peter K Hankard3, Linsey J Lister3, Stephen R Stürzenbaum5, A John Morgan1, David J Spurgeon3, Mark L Blaxter*2 and Peter Kille1 Address: 1Cardiff School of Biosciences, BIOSI 1, University of Cardiff, P.O. Box 915, Cardiff, CF10 3TL, UK, 2Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3JT, UK, 3Centre for Ecology and Hydrology, Monks Wood, Abbots Ripton, Huntingdon, Cambridgeshire, PE28 2LS, UK, 4Microarray Department and Integrative Bioinformatics Unit, Faculty of Science, University of Amsterdam, Kruislaan 318, Building I, Room 105C, 1098 SM Amsterdam, The Netherlands and 5School of Biomedical and Health Sciences, Pharmaceutical Sciences Division, Franklin Wilkins Building 150, Stamford St., London, SE1 9NH, UK Email: Jennifer Owen - [email protected]; B Ann Hedley - [email protected]; Claus Svendsen - [email protected]; Jodie Wren - [email protected]; Martijs J Jonker - [email protected]; Peter K Hankard - [email protected]; Linsey J Lister - [email protected]; Stephen R Stürzenbaum - [email protected]; A John Morgan - [email protected]; David J Spurgeon - [email protected]; Mark L Blaxter* - [email protected]; Peter Kille - [email protected] * Corresponding author †Equal contributors Published: 3 June 2008 Received: 16 October 2007 Accepted: 3 June 2008 BMC Genomics 2008, 9:266 doi:10.1186/1471-2164-9-266 This article is available from: http://www.biomedcentral.com/1471-2164/9/266 © 2008 Owen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: 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. Results: 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. Conclusion: 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. Page 1 of 21 (page number not for citation purposes) BMC Genomics 2008, 9:266 http://www.biomedcentral.com/1471-2164/9/266 Background From this transcriptome resource, we defined ~8100 Ever since Charles Darwin's classic work [1], earthworms genes, and have fabricated a cDNA microarray to investi- (Phylum Annelida, Class Oligochaeta) have been gate the transcriptome responses of L. rubellus through renowned as 'ecosystem engineers' in recognition of the normal growth and following sub-lethal exposure to a direct and indirect effects they have on water, nutrient and series of sub-lethal concentrations of Cd, FLA, and ATZ. carbon cycling in temperate and tropical soils [2]. Earth- From the derived transcript profiles we identify the key worms have therefore been widely adopted by interna- molecular responses and biochemical pathways associ- tional and national agencies for the diagnosis of soil ated with each life-stage treatment, and propose mecha- ecosystem health, and for predicting the potential envi- nisms of action for the three chemicals. ronmental impact of xenobiotics, such as industrial chem- icals, pesticides and medicines, from anthropogenic Results and Discussion sources [3]. Quantification of chemical toxicity to earth- Generation of ESTs from cDNA libraries spanning the L. worms currently relies on measuring the effects of expo- rubellus lifecycle and following exposure to target sure on key life-history traits (survival, growth, and chemicals reproduction) in standardised laboratory bioassays con- We generated 17,225 high-quality ESTs from nine differ- ducted with certain test species (Eisenia fetida, Eisenia ent cDNA libraries constructed from L. rubellus raised andrei and Lumbricus rubellus). These bioassays can pro- under defined conditions (Table 1 and Additional File 1; duce sensitive estimates of population effects, but are not all sequences are available in EMBL/GenBank/DDBJ and suited to elucidation of mechanisms of action, and thus in the project database LumbriBASE [see below]). We may be difficult to generalise from. For example, xenobi- maximised the gene discovery rate by screening out, from otic exposure may affect individual physiology, cocoon- some libraries, a small number of highly-expressed lay rates, cocoon viability and juvenile growth rates in a mRNAs (identified as clusters with many members after specific manner, resulting in different outcomes for popu- initial sequencing of ~4,000 ESTs). The ESTs were clus- lation growth rate and age structure. tered using the PartiGene suite of tools [17] and 8,129 clusters (different putative genes, named using permanent Complementing measurements of gross toxicity with identifiers of the form 'LRC#####') were defined. This molecular profiling and genomic studies can make plain number of putative genes is likely to be an overestimate the modes of action of specific xenobiotics and identify because (1) alternative splice forms may be assembled the generality of biological process affected as well as the into different clusters, (2) the partial nature of ESTs may molecular response pathways invoked [4-8]. Taking a spe- result in non-overlap between sequences from the same cific example, it has been observed that L. rubellus is able mRNA, and (3) our earthworms were drawn from an out- to colonise highly metal-contaminated environments bred source and allelic variation is likely. Within-dataset [8,9]. Detailed work identified that the primary molecules analyses suggested that the effects of these factors are responsible for this metal tolerance were earthworm met- minor, and that the true diversity in the dataset is ~8,000 allothioneins [10-15]. Though successful, the progress of different loci. If, like other non-vertebrates, L. rubellus has these mechanistic studies has been handicapped
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