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Mol Ecol Resour. 2016 Mar;16(2):470-9. doi: 10.1111/1755-0998.12472. Epub 2015 Oct 21.

Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis.

Liu S1,2,3, Wang X1,2, Xie L2, Tan M1,2, Li Z2, Su X1,4, Zhang H2, Misof B5, Kjer KM6, Tang M1,2, Niehuis O5, Jiang H2, Zhou X1,2.

Author information

1
China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
2
BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
3
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
4
Guizhou provincial Center For Disease Control And Prevention, Guiyang, Guizhou province, 550004, China.
5
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
6
Department of Entomology and Nematology, UC Davis, Davis, CA, 95616, USA.

Abstract

Biodiversity analyses based on next-generation sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of such a method is the lack of appropriate mitochondrial DNA enrichment ways. Because mitochondrial genomes (mitogenomes) make up only a small proportion of total DNA, PCR-free methods will inevitably result in a huge excess of data (>99%). Furthermore, the massive volume of sequence data is highly demanding on computing resources. Here, we present a mitogenome enrichment pipeline via a gene capture chip that was designed by virtue of the mitogenome sequences of the 1000 Insect Transcriptome Evolution project (1KITE, www.1kite.org). A mock sample containing 49 species was used to evaluate the efficiency of the mitogenome capture method. We demonstrate that the proportion of mitochondrial DNA can be increased by approximately 100-fold (from the original 0.47% to 42.52%). Variation in phylogenetic distances of target taxa to the probe set could in principle result in bias in abundance. However, the frequencies of input taxa were largely maintained after capture (R(2) = 0.81). We suggest that our mitogenome capture approach coupled with PCR-free shotgun sequencing could provide ecological researchers an efficient NGS method to deliver reliable biodiversity assessment.

KEYWORDS:

biodiversity; gene capture; microarray; mitochondrial genome

PMID:
26425990
DOI:
10.1111/1755-0998.12472
[Indexed for MEDLINE]

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