Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics
Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics
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DOI：
10.1093/sysbio/syx048
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发表时间：
2018-01-01
影响因子：
6.5
通讯作者：
Kawahara, Akito Y.
中科院分区：
文献类型：
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作者：
Breinholt, Jesse W.;Earl, Chandra;Kawahara, Akito Y.
下一代测序技术的出现使得可以收集大部分基因组用于系统发育分析。混合富集和转录组学是利用下一代测序的两种技术，并已显示出很大的前景。然而，处理混合富集数据的方法仍然有限。我们开发了一个管道，用于锚定混合富集（AHE）读取组装、直系同源确定、污染筛选和目标“探针”区域侧翼序列的数据处理。我们应用这种方法来研究蝴蝶和飞蛾（鳞翅目）的系统发育，这是一个由超过 157,000 个已描述物种组成的巨大多样性群体，但对其深层次系统发育关系知之甚少。我们推出了一种新的用于鳞翅目系统发育的 855 个位点 AHE 试剂盒，并将所得树与转录组中的树进行比较。该富集试剂盒是根据现有基因组、转录组和表达序列标签设计的，用于捕获 23 个鳞翅目科 54 个物种的序列数据。根据 AHE 数据估计的系统发育与转录组生成的树基本一致，为除了最深的分类水平之外的所有关系提供了强有力的支持。我们结合 AHE 和转录组数据生成了一个新的鳞翅目系统发育学，代表 42 个科的 76 个典型物种。这棵树为许多关系提供了强有力的支持，包括七个蝴蝶家族之间的关系。将 AHE 数据添加到现有的转录组数据集中降低了鳞翅目骨干上的节点支持，但将具有 AHE 数据的分类单元牢固地放置在系统发育上。将 AHE 测序的分类群与现有的转录组和基因组相结合，得到了一个对 (Calliduloidea + Gelechioidea + Thyridoidea) + (Papilionoidea + Pyraloidea + Macroheterocera) 具有强有力支持的树。为了在浅层分类水平上检验 AHE 的功效，还对代表最近分歧的姐妹类群土星科 (Saturniidae) 和天蛾科 (Sphingidae) 进行了系统发育分析。这些分析利用了探针区域的序列及其侧翼的数据，几乎使数据集的大小增加了一倍；由此产生的树支持新的系统发育关系，特别是在Saturniidae和Sphingidae中（例如，后者衍生的Hemarina）。我们希望我们的数据处理流程、混合富集基因集以及 AHE 数据与转录组相结合的方法将对更广泛的系统学社区有用。
The advent of next-generation sequencing technology has allowed for the collection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combineAHEand transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea + Gelechioidea + Thyridoidea) + (Papilionoidea + Pyraloidea + Macroheterocera). To examine the efficacy ofAHEat a shallowtaxonomic level, phylogenetic analyseswere also conducted on a sister group representing amore recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community.