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Ultrasequencing of the meiofaunal biosphere practice, pitfalls and promises

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dc.contributor.authorCreer, S.
dc.contributor.authorFonseca, V. G.
dc.contributor.authorPorazinska, D. L.
dc.contributor.authorGiblin-Davis, R. M.
dc.contributor.authorSung, W.
dc.contributor.authorPower, Deborah
dc.contributor.authorPacker, Margaret
dc.contributor.authorCarvalho, Gary
dc.contributor.authorBlaxter, M. L.
dc.contributor.authorLambshead, P. J. D.
dc.contributor.authorThomas, W. K.
dc.date.accessioned2014-10-24T12:42:34Z
dc.date.available2014-10-24T12:42:34Z
dc.date.issued2010
dc.description.abstractBiodiversity assessment is the key to understanding the relationship between biodiversity and ecosystem functioning, but there is a well-acknowledged biodiversity identification gap related to eukaryotic meiofaunal organisms. Meiofaunal identification is confounded by the small size of taxa, morphological convergence and intraspecific variation. However, the most important restricting factor in meiofaunal ecological research is the mismatch between diversity and the number of taxonomists that are able to simultaneously identify and catalogue meiofaunal diversity. Accordingly, a molecular operational taxonomic unit (MOTU)-based approach has been advocated for en mass meiofaunal biodiversity assessment, but it has been restricted by the lack of throughput afforded by chain termination sequencing. Contemporary pyrosequencing offers a solution to this problem in the form of environmental metagenetic analyses, but this represents a novel field of biodiversity assessment. Here, we provide an overview of meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction to PCR, sequencing and the bioinformatic interrogation of multiple, independent samples using 454 Roche sequencing platforms. We report two examples of environmental metagenetic nuclear small subunit 18S (nSSU) analyses of marine and tropical rainforest habitats and provide critical appraisals of the level of putative recombinant DNA molecules (chimeras) in metagenetic data sets. Following stringent quality control measures, environmental metagenetic analyses achieve MOTU formation across the eukaryote domain of life at a fraction of the time and cost of traditional approaches. The effectiveness of Roche 454 sequencing brings substantial advantages to studies aiming to elucidate the molecular genetic richness of not only meiofaunal, but also all complex eukaryotic communities.por
dc.description.sponsorshipWe would like to thank Neil Hall, Andrew Cossins and Margaret Hughes of the Liverpool Advanced Molecular Genetic Facility for 454 sequencing support, in addition to the staff of Edinburgh University’s Gene Pool sequencing service and Holly Bik for field support. Further thanks go to Emlyn Roberts, Wendy Grail and technical support staff at Bangor University. We also thank the Organization for Tropical Studies for access to the La Selva Biological Station sampling plots, Alejandro Esquivel from Universidad Nacional and Thomas O. Powers from the University of Nebraska for technical assistance while in Costa Rica, and Regina Shaw and Bill Farmerie for 454 sequencing support at ICBR, University of Florida. This work was supported by a Natural Environment Research Council (NERC) New Investigator Grant (NE ⁄ E001505 ⁄ 1) and a Post Genomic and Proteomics Grant (NE ⁄ F001266 ⁄ 1) to SC, an FCT Grant to VGF (SFRH ⁄ BD ⁄ 27413 ⁄ 2006) and a USDA⁄ CSREES–TSTAR Grant 2006-04347 (FLA-FTL-04544) and National Science Foundation (NSF) Biotic Surveys and Inventories projects (DEB-0450537; DEB- 0640807) to RMGD.por
dc.identifier.citationCreer S, Fonseca VG, Porazinska DL, Giblin-Davis RM, Sung W, Power DM, Packer M, Carvalho GR, Blaxter ML, Lambshead PJ, Thomas WK., "Ultrasequencing of the meiofaunal biosphere Practice, pitfalls and promises" in Mol Ecol. 2010 Mar;19 Suppl 1:4-20.por
dc.identifier.doihttp://dx.doi.org/10.1111/j.1365-294X.2009.04473.x
dc.identifier.issn0962-1083
dc.identifier.otherAUT: DPO00386;
dc.identifier.urihttp://hdl.handle.net/10400.1/5481
dc.language.isoengpor
dc.peerreviewedyespor
dc.publisherWileypor
dc.subject454 environmental sequencingpor
dc.subjectMeiofaunal and eukaryotic biodiversitypor
dc.subjectMetageneticspor
dc.subjectMetagenomicspor
dc.titleUltrasequencing of the meiofaunal biosphere practice, pitfalls and promisespor
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage20por
oaire.citation.issueSuppl 1por
oaire.citation.startPage4por
oaire.citation.titleMolecular Ecologypor
oaire.citation.volume19por
person.familyNamePower
person.givenNameDeborah Mary
person.identifier.ciencia-id891A-8A44-3CAE
person.identifier.orcid0000-0003-1366-0246
person.identifier.scopus-author-id7101806760
rcaap.rightsrestrictedAccesspor
rcaap.typearticlepor
relation.isAuthorOfPublicationc68f5ffb-63f6-4c70-8957-29e464fb59c0
relation.isAuthorOfPublication.latestForDiscoveryc68f5ffb-63f6-4c70-8957-29e464fb59c0

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