Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

Molecular Ecology - Tập 19 Số s1 - Trang 4-20 - 2010
Simon Creer1, Vera G. Fonseca2, Dorota L. Porazinska3, Robin M. Giblin-davis3, Way Sung4, Deborah M. Power5, Margaret Packer6, Gary R. Carvalho2, Mark Blaxter7, David T. Bilton8, W. Kelley Thomas4
1Environment Centre Wales, Bangor University, Gwynedd, UK
2School of Biological Sciences, Environment Centre Wales, Deiniol Road, College of Natural Sciences, Bangor University, Gwynedd, LL57 2UW, UK
3Fort Lauderdale Research and Education Center, University of Florida, IFAS, 3205 College Avenue, Fort Lauderdale, FL 33314, USA
4Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Durham, NH, 03824, USA
5Centre of Marine Sciences, CCMAR–CIMAR Associate Laboratory, University of Algarve, Gambelas, 8005‐139 Faro, Portugal
6Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
7Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3JT, UK
8School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK

Tóm tắt

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.

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Molecular Ecology

Tập 19 Số s1

4-20

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