Mitochondrial metagenomics: letting the genes out of the bottle.
Mitochondrial metagenomics: letting the genes out of the bottle.
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DOI：
10.1186/s13742-016-0120-y
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发表时间：
2016
期刊：
影响因子：
9.2
通讯作者：
Vogler AP
中科院分区：
文献类型：
--
作者：
Crampton-Platt A;Yu DW;Zhou X;Vogler AP
“线粒体宏基因组学”（MMG）是一种从样本混合物中对总DNA进行鸟枪测序并随后对线粒体序列进行生物信息学提取的方法。该方法可应用于系统发育分析的分类学选择的类群，作为一个经济的替代有丝分裂基因组测序从个别物种，或环境样品的混合标本，如从大规模诱捕无脊椎动物。线粒体基因组序列的常规生成在系统学和群落遗传学上都具有巨大的潜力。对环境样品进行低覆盖率鸟枪测序的读数绘图也使得有可能获得全群落系统发育和物种组成的空间和时间周转数据，即使是在物种一级分类和生物多样性模式知之甚少的复杂生态系统中。此外，读段作图可以产生关于物种生物量的信息，并且可能允许量化物种内遗传变异。MMG的成功依赖于许多线粒体基因组重叠群的形成，这可以用标准基因组组装器实现，但是组装效率仍然存在各种挑战，特别是在面对可变的相对物种丰度和种内遗传变异时。然而，一些研究已经证明了MMG的有丝分裂基因组的力量，用于准确的系统发育定位，物种特征的进化分析，生物多样性发现和物种分布模式的建立;它为统一物种多样性的生态和进化理解提供了一个有前途的途径。
‘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.