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The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera
B. Linard, A. Crampton-Platt, J. Moriniere, MJTN. Timmermans, C. Andújar, P. Arribas, KE. Miller, J. Lipecki, E. Favreau, A. Hunter, C. Gómez-Rodríguez, C. Barton, R. Nie, CPDT. Gillett, T. Breeschoten, L. Bocak, AP. Vogler,
Jazyk angličtina Země Spojené státy americké
Typ dokumentu časopisecké články, práce podpořená grantem
- MeSH
- algoritmy MeSH
- brouci klasifikace genetika MeSH
- databáze genetické MeSH
- fylogeneze * MeSH
- metagenomika * MeSH
- mitochondrie genetika MeSH
- sekvence nukleotidů MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.
Bavarian State Collection of Zoology Münchhausenstrasse 21 81247 München Germany
Chemistry Department University of Warwick Coventry UK
Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
Department of Life Sciences Natural History Museum London SW7 5BD United Kingdom
Department of Life Sciences Silwood Park Campus Imperial College London Ascot SL5 7PY United Kingdom
Department of Natural Sciences Hendon Campus Middlesex University London NW4 4BT United Kingdom
ISEM Univ Montpellier CNRS IRD EPHE CIRAD INRAP Montpellier France
Island Ecology and Evolution Research Group IPNA CSIC 38206 La Laguna Tenerife Canary Islands Spain
Leibniz Institute for Zoo and Wildlife Research Alfred Kowalke Strasse 17 10315 Berlin Germany
LIRMM Univ Montpellier CNRS Montpellier France
Naturalis Biodiversity Center Darwinweg 2 2333 CR Leiden The Netherlands
Research Services The University of Kent Canterbury Kent CT6 7NZ UK
School of Biological and Chemical Sciences Queen Mary University of London London UK
Citace poskytuje Crossref.org
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- $a Linard, Benjamin $u Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom; LIRMM, Univ. Montpellier, CNRS, Montpellier, France(1); ISEM, Univ. Montpellier, CNRS, IRD, EPHE, CIRAD, INRAP, Montpellier, France(1). Electronic address: benjamin.linard@lirmm.fr.
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- $a Crampton-Platt, Alex $u Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom; Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot SL5 7PY, United Kingdom; Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany(1).
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