title: Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis.
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.
authors.affiliation: China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.|BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.|Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
authors.forename: Shanlin
authors.initials: S
authors.lastname: Liu
authors.affiliation: China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.|BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Xie
authors.affiliation: China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.|BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
authors.forename: Meihua
authors.initials: M
authors.lastname: Tan
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Li
authors.affiliation: China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.|Guizhou provincial Center For Disease Control And Prevention, Guiyang, Guizhou province, 550004, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Su
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Misof
authors.affiliation: Department of Entomology and Nematology, UC Davis, Davis, CA, 95616, USA.
authors.forename: Karl M
authors.initials: KM
authors.lastname: Kjer
authors.affiliation: China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.|BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
authors.forename: Min
authors.initials: M
authors.lastname: Tang
authors.affiliation: Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Niehuis
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Jiang
authors.affiliation: China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.|BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhou
mesh_terms: D000818:Animals; D044822:Biodiversity; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification*; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D007313:Insecta / Q000235:genetics; D008928:Mitochondria / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004272:DNA, Mitochondrial
keywords: biodiversity; gene capture; microarray; mitochondrial genome