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首页> 外文期刊>Genome research >Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens.
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Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens.

机译：高效的跨物种捕获非侵入性采样博物馆标本的线粒体基因组杂交和下一代测序。

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摘要

The ability to uncover the phylogenetic history of recently extinct species and other species known only from archived museum material has rapidly improved due to the reduced cost and increased sequence capacity of next-generation sequencing technologies. One limitation of these approaches is the difficulty of isolating and sequencing large, orthologous DNA regions across multiple divergent species, which is exacerbated for museum specimens, where DNA quality varies greatly between samples and contamination levels are often high. Here we describe the use of cross-species DNA capture hybridization techniques and next-generation sequencing to selectively isolate and sequence partial to full-length mitochondrial DNA genomes from the degraded DNA of museum specimens, using probes generated from the DNA of a single extant species. We demonstrate our approach on specimens from an enigmatic gliding mammal, the Sunda colugo, which is widely distributed throughout Southeast Asia. We isolated DNA from 13 colugo specimens collected 47-170 years ago, and successfully captured and sequenced mitochondrial DNA from every specimen, frequently recovering fragments with 10%-13% sequence divergence from the capture probe sequence. Phylogenetic results reveal deep genetic divergence among colugos, both within and between the islands of Borneo and Java, as well as between the Malay Peninsula and different Sundaic islands. Our method is based on noninvasive sampling of minute amounts of soft tissue material from museum specimens, leaving the original specimen essentially undamaged. This approach represents a paradigm shift away from standard PCR-based approaches for accessing population genetic and phylogenomic information from poorly known and difficult-to-study species.
机译：由于降低了成本并提高了下一代测序技术的测序能力，揭露最近灭绝的物种和仅从已存档的博物馆资料中得知的其他物种的系统发生历史的能力已得到迅速提高。这些方法的局限性是难以对多个不同物种中的大型直系同源DNA区域进行分离和测序，这对于博物馆标本更为严重，因为博物馆标本之间的DNA质量差异很大，污染水平通常很高。在这里，我们描述了使用跨物种DNA捕获杂交技术和下一代测序技术，使用从单个现存物种的DNA产生的探针，从博物馆标本的降解DNA中选择性分离和测序部分至全长线粒体DNA基因组。 。我们在神秘的滑行哺乳动物Sunda colugo的标本上展示了我们的方法，该标本广泛分布于整个东南亚。我们从47-170年前收集的13个colugo标本中分离了DNA，并成功地从每个标本中捕获并测序了线粒体DNA，经常从捕获探针序列中回收具有10％-13％序列差异的片段。系统发育研究结果表明，婆罗洲和爪哇岛之间以及之间，马来半岛和不同的圣代岛之间，孔雀犬之间存在着深远的遗传差异。我们的方法是基于无创取样的博物馆标本中的微量软组织材料，而原始标本基本上没有损坏。该方法代表了从基于PCR的标准方法转变的范式，该方法用于从鲜为人知且难以研究的物种中获取种群遗传和系统信息。

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