A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology
A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology
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DOI：
10.1007/s10764-013-9663-2
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发表时间：
2013-04-01
影响因子：
2.5
通讯作者：
Burrell, Andrew S.
中科院分区：
文献类型：
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作者：
Bergey, Christina M.;Pozzi, Luca;Burrell, Andrew S.
在过去的二十年里，灵长类动物学家已经受益于使用大量的分子标记来研究灵长类动物行为和进化历史的各个方面。然而，迄今为止的大多数研究都是基于单个基因座，通常是线粒体DNA，或一些核标记，例如，微型卫星不幸的是，这些标记的使用不仅不能成功地解决灵长类群体遗传学和灵长类动物遗传学中的重要问题（主要是因为基因树和物种树之间的不一致），而且它们的开发往往是一项耗时且昂贵的任务。下一代测序技术的出现使研究人员能够为非模式生物生成大量的基因组数据。然而，全基因组测序对于大多数灵长类物种来说仍然成本高昂。在这里，我们介绍了第二代测序技术，用于对非模式生物的数千个全基因组标记进行基因分型。限制性位点相关DNA测序（RAD-seq）降低了基因组的复杂性，并允许在许多个体中廉价快速地发现数千个标记。在这里，我们描述了这项技术的原理，我们展示了它在五种灵长类动物，Microcebus sp.，Cebus sp.，狮尾古猿（Theropithecus gelada）、黑猩猩（Pan troglodytes）和智人（Homo sapiens），代表了该目中的一些主要谱系。尽管存在技术和生物信息学挑战，但RAD-seq是灵长类动物多位点系统发育和群体遗传研究的一种有前途的方法，特别是在年轻的进化枝中，其中可能在群体或物种中发现大量直系同源区域。
Over the last two decades primatologists have benefited from the use of numerous molecular markers to study various aspects of primate behavior and evolutionary history. However, most of the studies to date have been based on a single locus, usually mitochondrial DNA, or a few nuclear markers, e.g., microsatellites. Unfortunately, the use of such markers not only is unable to address successfully important questions in primate population genetics and phylogenetics (mainly because of the discordance between gene tree and species tree), but also their development is often a time-consuming and expensive task. The advent of next-generation sequencing allows researchers to generate large amounts of genomic data for nonmodel organisms. However, whole genome sequencing is still cost prohibitive for most primate species. We here introduce a second-generation sequencing technique for genotyping thousands of genome-wide markers for nonmodel organisms. Restriction site-associated DNA sequencing (RAD-seq) reduces the complexity of the genome and allows inexpensive and fast discovery of thousands of markers in many individuals. Here, we describe the principles of this technique and we demonstrate its application in five primates, Microcebus sp., Cebus sp., Theropithecus gelada, Pan troglodytes, and Homo sapiens, representing some of the major lineages within the order. Despite technical and bioinformatic challenges, RAD-seq is a promising method for multilocus phylogenetic and population genetic studies in primates, particularly in young clades in which a high number of orthologous regions are likely to be found across populations or species.