Linard Benjamin, Crampton-Platt Alex, Gillett Conrad P D T, Timmermans Martijn J T N, Vogler Alfried P
Department of Life Sciences, Natural History Museum, London, United Kingdom.
Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Genetics, Evolution and Environment, University College London, United Kingdom.
Genome Biol Evol. 2015 May 14;7(6):1474-89. doi: 10.1093/gbe/evv086.
Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from low-coverage sequencing by "genome skimming," which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and known repeat elements of high and low complexity, including numerous copies of rRNA and histone genes. Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous "clusters" of scaffolds mapped to the same genomic site revealed intra- and/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The "metagenome skimming" approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics.
宏基因组分析在后生动物中具有挑战性，但通过“基因组略读”可以从低覆盖度测序中组装高拷贝数和重复区域，本文将其作为一种表征在生态或分类背景下获得的宏基因组的新方法。对两个各有约200种鞘翅目（甲虫）样本池进行的Illumina鸟枪法测序被组装成了数万个支架。重复的低覆盖度测序始终能获得相似的支架集，尽管约70%的支架无法与现有的基因组数据库比对识别。可识别的支架包括线粒体DNA、与表达序列标签和蛋白质数据库比对有匹配的保守序列，以及已知的高低复杂度重复元件，包括众多rRNA和组蛋白基因的拷贝。组蛋白的组装捕获了鞘翅目中多样的基因顺序和一级序列。与小蠹虫和赤拟谷盗现有鞘翅目基因组序列中多个位点相似的支架显示出这些支架对这两个基因组中任意一个的高度特异性，特别是对于高拷贝数重复序列。许多映射到同一基因组位点的支架“簇”揭示了宏基因组样本池内的基因组内和/或基因组间变异。除了宏基因组分类组成的影响外，映射支架的数量还揭示了两个参考基因组之间的结构差异，尽管这一显著发现的意义尚不清楚。最后，还回收了明显的外源序列，包括潜在的食用植物、真菌病原体和细菌共生体。“基因组略读”方法有助于捕获研究较少、物种丰富的谱系的基因组多样性，并为环境基因组学开辟了新前景。
