Sequence capture using AFLP-generated baits: A cost-effective method for high-throughput phylogenetic and phylogeographic analysis
Sequence capture using AFLP-generated baits: A cost-effective method for high-throughput phylogenetic and phylogeographic analysis
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使用 AFLP 生成的诱饵进行序列捕获：一种用于高通量系统发育和系统地理学分析的经济有效的方法
DOI：
10.1002/ece3.5176
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发表时间：
2019
影响因子：
2.6
通讯作者：
Zhang Peng
中科院分区：
文献类型：
--
作者：
Li Jia Xuan;Zeng Zhao Chi;Wang Ying Yong;Liang Dan;Zhang Peng
靶序列捕获是富集特定基因组区域的有效技术，用于生态学和进化研究中的高通量测序。近年来，人们提出了许多序列捕获方法，但大多数方法都依赖于商业合成诱饵，这使得实验费用昂贵。在这里，我们提出了一种新的序列捕获方法，称为基于AFLP的基因组序列捕获（AFLP捕获）。该方法利用AFLP（扩增片段长度多态性）技术生成自制的捕获诱饵，而不需要预先的基因组信息，因此适用于任何生物。在该方法中，代表基因组的随机部分的生物素化AFLP片段用作诱饵以从基因组鸟枪测序文库捕获同源片段。在一项试验研究中，我们利用AFLP Capture技术成功地从11种臭蛙中获得了511个正向多态性位点（总长度> 700，000 bp），并在4个臭蛙个体中获得了超过100，000个单核苷酸多态性（SNP）。这一结果表明，我们的方法可以用来解决各种进化深度的问题（从种间水平到种内水平）。我们还讨论了诱饵制备的灵活性以及如何分析测序数据。总之，AFLP Capture是一种快速灵活的工具，可以显著降低需要分析基因组规模数据（数百或数千个位点）的系统发育研究的实验成本。
Target sequence capture is an efficient technique to enrich specific genomic regions for high‐throughput sequencing in ecological and evolutionary studies. In recent years, many sequence capture approaches have been proposed, but most of them rely on commercial synthetic baits which make the experiment expensive. Here, we present a novel sequence capture approach called AFLP‐based genome sequence capture (AFLP Capture). This method uses the AFLP (amplified fragment length polymorphism) technique to generate homemade capture baits without the need for prior genome information, thus is applicable to any organisms. In this approach, biotinylated AFLP fragments representing a random fraction of the genome are used as baits to capture the homologous fragments from genomic shotgun sequencing libraries. In a trial study, by using AFLP Capture, we successfully obtained 511 orthologous loci (>700,000 bp in total length) from 11Odorranaspecies and more than 100,000 single nucleotide polymorphisms (SNPs) in four analyzed individuals of anOdorranaspecies. This result shows that our method can be used to address questions of various evolutionary depths (from interspecies level to intraspecies level). We also discuss the flexibility in bait preparation and how the sequencing data are analyzed. In summary, AFLP Capture is a rapid and flexible tool and can significantly reduce the experimental cost for phylogenetic studies that require analyzing genome‐scale data (hundreds or thousands of loci).