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Gigascience. 2016 Mar 22;5:15. doi: 10.1186/s13742-016-0120-y. eCollection 2016.

Mitochondrial metagenomics: letting the genes out of the bottle.

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Department of Life Sciences, Natural History Museum, London, SW7 5BD UK ; Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT UK.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, Yunnan Province 650223 China ; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ UK.
China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province 518083 China.
Department of Life Sciences, Natural History Museum, London, SW7 5BD UK ; Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY UK.


'Mitochondrial metagenomics' (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity.


Biodiversity; Community ecology; Genome assembly; Illumina; Phylogenetics; Shotgun sequencing

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