Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages
Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages
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DOI：
10.1111/2041-210x.12376
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发表时间：
2015-08-01
影响因子：
6.6
通讯作者：
Vogler, Alfried P.
中科院分区：
文献类型：
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作者：
Gomez-Rodriguez, Carola;Crampton-Platt, Alex;Vogler, Alfried P.
1. 节肢动物混合物种样本的生物多样性可以通过对大量基因组 DNA 进行鸟枪法测序以及随后对线粒体基因组进行生物信息学组装来表征。在这里，我们通过对来自 10 个群落的超过 2600 只叶甲虫（叶甲科）个体的混合物进行 Illumina 测序来测试线粒体宏基因组的威力。2。通过读取与三个参考数据库的匹配来评估物种丰富度、群落差异和生物量的模式，包括 (i) 为 156 个物种（占研究中物种的 89%）生成的一组定制的线粒体基因组； (ii) 通过从头组装来自现实世界社区的序列读数而获得的有丝分裂基因组； (iii) 一组定制的 DNA 条形码 (cox1-5) 序列。3．针对定制参考基因组的物种检测非常高 (>90%)。对于有丝分裂基因组，错误存在很少见，但对于条形码参考，错误存在略高。错误缺席主要是由于参考数据库的不完整性，因此在从头数据集中更为普遍。生物量（丰度x身体长度）和读数数量密切相关，证明了线粒体宏基因组学在物种丰度研究中的潜力。4．丝裂基因组的系统发育树显示出与叶科已知关系的高度一致性。位点之间的分类学和系统发育差异模式与形态学鉴定数据高度一致。5．线粒体宏基因组学的力量源于从样本混合物中快速组装线粒体基因组的可能性，以及使用读数计数直接从社区样本中准确估计生物多样性的关键参数。
1. The biodiversity of mixed-species samples of arthropods can be characterized by shotgun sequencing of bulk genomic DNA and subsequent bioinformatics assembly of mitochondrial genomes. Here, we tested the power of mitochondrial metagenomics by conducting Illumina sequencing on mixtures of >2600 individuals of leaf beetles (Chrysomelidae) from 10 communities.2. Patterns of species richness, community dissimilarity and biomass were assessed from matches of reads against three reference databases, including (i) a custom set of mitogenomes generated for 156 species (89% of species in the study); (ii) mitogenomes obtained by the de novo assembly of sequence reads from the real-world communities; and (iii) a custom set of DNA barcode (cox1-5) sequences.3. Species detection against the custom-built reference genomes was very high (>90%). False presences were rare against mitogenomes but slightly higher against the barcode references. False absences were mainly due to the incompleteness of the reference databases and, thus, more prevalent in the de novo data set. Biomass (abundancexbody length) and read numbers were strongly correlated, demonstrating the potential of mitochondrial metagenomics for studies of species abundance.4. A phylogenetic tree from the mitogenomes showed high congruence with known relationships in Chrysomelidae. Patterns of taxonomic and phylogenetic dissimilarity between sites were highly consistent with data from morphological identifications.5. The power of mitochondrial metagenomics results from the possibility of rapid assembly of mitogenomes from mixtures of specimens and the use of read counts for accurate estimates of key parameters of biodiversity directly from community samples.