Sequence capture of ultraconserved elements from bird museum specimens
Sequence capture of ultraconserved elements from bird museum specimens
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DOI：
10.1111/1755-0998.12466
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发表时间：
2016-09-01
影响因子：
7.7
通讯作者：
Faircloth, Brant C.
中科院分区：
文献类型：
--
作者：
McCormack, John E.;Tsai, Whitney L. E.;Faircloth, Brant C.
新的DNA测序技术使研究人员能够探索分子时代之前收集的数百万自然历史标本的基因组。然而，我们对特定的下一代测序（NGS）技术如何处理通常从博物馆标本中提取的降解DNA知之甚少。在这里，我们使用一种类型的NGS方法，序列捕获的超保守元素（UCEs），收集数据，从鸟类博物馆标本，年龄为120岁。我们有针对性地在27个西部灌丛鸦（Aphelocoma californica）代表三个进化谱系，可能是物种的5060 UCE位点，我们收集了平均3749个UCE位点，含有4460个单核苷酸多态性（SNP）。尽管老标本产生较少和较短的基因座一般，我们收集了数千个标记，即使是最古老的标本。每个个体更多的测序读数有助于增加我们从旧标本中回收的UCE基因座的数量，但更多的测序在增加基因座长度方面并不成功。我们在一些样本中检测到污染，并确定污染在测序较少的旧样本中更普遍。对于从串联UCE基因座产生的同源性，污染导致一些个体的不正确放置。相比之下，由UCE基因座内的SNP构建的物种树正确地将个体置于三个单系群中，这可能是因为SNP调用使用了更严格的分析程序。这项研究和其他最近关于博物馆标本基因组学的研究对自然历史收藏有着深远的影响，数百万古老的标本现在应该被视为基因组资源。
New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120years. We targeted 5060 UCE loci in 27 western scrub-jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources.