A rapid and cost-effective approach for the development of polymorphic microsatellites in non-model species using paired-end RAD sequencing
A rapid and cost-effective approach for the development of polymorphic microsatellites in non-model species using paired-end RAD sequencing
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使用双端 RAD 测序在非模型物种中开发多态性微卫星的快速且经济有效的方法
DOI：
10.1007/s00438-017-1337-x
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发表时间：
2017-06
期刊：
影响因子：
--
通讯作者：
Liu Jin-Xian
中科院分区：
文献类型：
--
作者：
Xue Dong-Xiu;Li Yu-Long;Liu Jin-Xian
微卫星作为一种信息量最大、用途最广的DNA标记，已广泛应用于种群和保护遗传学研究。然而，微型卫星的开发传统上是费力、耗时和昂贵的。本研究以糙皮杜父鱼Trachidermus fasciatus为代表，建立了一种快速高效的“RAD-seq-Assembly-Microsatellite”微卫星标记筛选方法。通过限制性位点相关DNA测序（RAD-seq）产生的重叠配对末端Illumina读数基于含有限制性酶识别位点的读数的相似性进行聚类，然后组装成重叠群，其用于微卫星发现和引物设计。共产生121，750个RAD重叠群，平均长度为522 bp，19，782个重叠群包含微卫星基序。基于16，497个含有引物位点的重叠群，共成功设计了156，150对引物。对随机选取的52个微卫星位点进行验证，结果表明，45个位点（86.54%）在两个地理隔离的群体中扩增出多态性位点。带条肌与传统的基于DNA克隆的方法和其他基于新一代测序的方法相比，我们开发的新方法可以获得数千个微卫星位点，并且具有更高的成功扩增率和更低的成本，特别是对于基因组信息背景较浅的非模式物种。“RAD-seq-Assembly-Microsatellite”方法在未来非模式物种的生态学和进化研究中为微卫星开发带来了巨大的希望。
As one of the most informative and versatile DNA-based markers, microsatellites have been widely used in population and conservation genetic studies. However, the development of microsatellites has traditionally been laborious, time-consuming, and expensive. In the present study, a rapid and cost-effective “RAD-seq-Assembly-Microsatellite” approach was developed to identify abundant microsatellite markers in non-model species using the roughskin sculpinTrachidermus fasciatusas a representative. Overlapping paired-end Illumina reads generated by restriction-site-associated DNA sequencing (RAD-seq) were clustered based on the similarity of reads containing the restriction enzyme recognition site and then assembled into contigs, which were used for microsatellite discovery and primer design. A total of 121,750 RAD contigs were generated with a mean length of 522 bp, and 19,782 contigs contained microsatellite motifs. A total of 156,150 primer pairs were successfully designed based on 16,497 contigs containing priming sites. Experimental validation of 52 randomly selected microsatellite loci demonstrated that 45 (86.54%) loci were successfully amplified and polymorphic in two geographically isolated populations ofT. fasciatus. Compared with traditional approaches based on DNA cloning and other approaches based on next-generation sequencing, our newly developed approach could yield thousands of microsatellite loci with much higher successful amplification rate and lower costs, especially for non-model species with shallow background of genomic information. The “RAD-seq-Assembly-Microsatellite” approach holds great promise for microsatellite development in future ecological and evolutionary studies of non-model species.
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影响因子：
7.7
作者：
Castoe TA;Poole AW;Gu W;Jason de Koning AP;Daza JM;Smith EN;Pollock DD
通讯作者：
Pollock DD
DOI：
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发表时间：
2002
期刊：
--
影响因子：
--
作者：
Stephen D. E. Park
通讯作者：
Stephen D. E. Park
影响因子：
3.1
作者：
S. Montanari;L. Perchepied;Déborah Renault;L. Frijters;R. Velasco;M. Horner;S. Gardiner;D. Chagné;V. Bus;C. Durel;M. Malnoy
通讯作者：
S. Montanari;L. Perchepied;Déborah Renault;L. Frijters;R. Velasco;M. Horner;S. Gardiner;D. Chagné;V. Bus;C. Durel;M. Malnoy
DOI：
10.4238/gmr.15017550
发表时间：
2016-02
期刊：
Genetics and molecular research : GMR
影响因子：
--
作者：
Yang Xy;Long Zc;A. W. Gichira;Guo Yh;Qing‐Feng Wang;Jin‐Ming Chen
通讯作者：
Yang Xy;Long Zc;A. W. Gichira;Guo Yh;Qing‐Feng Wang;Jin‐Ming Chen
使用下一代测序开发日本糖精基因组 SSR 标记
影响因子：
3.3
作者：
Li, Qiuying;Zhang, Jie;Duan, Delin
通讯作者：
Duan, Delin