Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics.
Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics.
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DOI：
10.1093/gbe/evv086
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发表时间：
2015-05-14
影响因子：
3.3
通讯作者：
Vogler AP
中科院分区：
文献类型：
--
作者：
Linard B;Crampton-Platt A;Gillett CP;Timmermans MJ;Vogler AP
宏基因组分析是具有挑战性的后生动物，但高拷贝数和重复区域可以组装从低覆盖率测序的“基因组略读”，这是应用在这里作为一种新的方式来表征宏基因组获得的生态或分类背景。对两个鞘翅目（甲虫）池进行的Illumina鸟枪测序，每个池约有200个物种，组装成数万个支架。重复的低覆盖率测序一致地恢复了类似的支架组，尽管大约70%的支架不能在现有的基因组数据库中识别。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匹配的保守序列，以及已知的高复杂性和低复杂性的重复元件，包括rRNA和组蛋白基因的大量拷贝。组蛋白集合体捕获了鞘翅目昆虫基因序列和一级序列的多样性。与可获得的鞘翅目基因组序列中的多个位点相似的Dendroctonus和Tribolium的支架揭示了支架对这些基因组中的任一个的高特异性，特别是对于高拷贝数重复。映射到相同基因组位点的支架的许多“簇”揭示了宏基因组池内的基因组内和/或基因组间变异。除了宏基因组的分类组成的影响，映射的支架的数量也揭示了两个参考基因组之间的结构差异，尽管这一惊人发现的意义尚不清楚。最后，显然是外源序列恢复，包括潜在的粮食植物，真菌病原体和细菌共生体。“宏基因组略读”方法对于捕获研究不足、物种丰富的谱系的基因组多样性很有用，并开辟了环境基因组学的新前景。
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.
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影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
--
作者：
Lee MH;Lee SW
通讯作者：
Lee SW
影响因子：
14.9
作者：
Benson DA;Cavanaugh M;Clark K;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
影响因子：
12.3
作者：
Keeling CI;Yuen MM;Liao NY;Docking TR;Chan SK;Taylor GA;Palmquist DL;Jackman SD;Nguyen A;Li M;Henderson H;Janes JK;Zhao Y;Pandoh P;Moore R;Sperling FA;Huber DP;Birol I;Jones SJ;Bohlmann J
通讯作者：
Bohlmann J
影响因子：
3.8
作者：
Foret, Sylvain;Wanner, Kevin W.;Maleszka, Ryszard
通讯作者：
Maleszka, Ryszard