Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics.
Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics.
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DOI：
10.1111/mec.12228
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发表时间：
2013-06
影响因子：
4.9
通讯作者：
Shank TM
中科院分区：
文献类型：
--
作者：
Reitzel AM;Herrera S;Layden MJ;Martindale MQ;Shank TM
描述基因组中大量的单核苷酸多态(SNPs)可以加深对种群人口历史的理解，并识别在自然种群中选择的基因组区域。为此，利用下一代测序的力量来了解海洋无脊椎动物的生态和进化的种群基因组方法是测试海洋生物学和保护中长期存在的问题的福音。我们使用限制性内切酶相关DNA测序技术(RAD-seq)在海葵的自然种群中确定了SNPs，这是一种新兴的线虫模式，在北美和南美洲的河口生境以及英国的部分地区具有广泛的地理范围。我们在从新斯科舍省到南卡罗来纳州四个地点的30个条形码个体的数千个RAD基因座中识别出数百个含有SNP的标签。使用高置信度SNPs的种群基因组分析导致了高度分辨的系统地理学，这是以前使用传统标记进行的研究所没有达到的结果。位点特异性FST与杂合性的关系图表明，大多数多态位点是中性的，较小的比例表明存在平衡选择的证据。被推测为选择不平衡的基因座被定位到基因组上，其中90%位于基因体中，表明了潜在的选择目标。有和没有参考基因组的分析结果支持类似的结论，进一步支持RAD-SEQ作为一种可以有效应用于缺乏现有基因组资源的物种的方法。我们讨论了RAD-SEQ方法在新兴线虫研究以及其他线虫物种，特别是珊瑚中的应用，以确定种群的系统地理关系和识别正在进行选择的基因组区域。
Characterization of large numbers of single nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions under selection in natural populations. To this end, population genomic approaches that harness the power of next-generation sequencing to understand the ecology and evolution of marine invertebrates represent a boon to test long-standing questions in marine biology and conservation. We employed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs in natural populations of the sea anemone Nematostella vectensis, an emerging cnidarian model with a broad geographic range in estuarine habitats in North and South America, and portions of England. We identified hundreds of SNP-containing tags in thousands of RAD loci from 30 barcoded individuals inhabiting four locations from Nova Scotia to South Carolina. Population genomic analyses using high-confidence SNPs resulted in a highly-resolved phylogeography, a result not achieved in previous studies using traditional markers. Plots of locus-specific FST against heterozygosity suggest that a majority of polymorphic sites are neutral, with a smaller proportion suggesting evidence for balancing selection. Loci inferred to be under balancing selection were mapped to the genome, where 90% were located in gene bodies, indicating potential targets of selection. Results from analyses with and without a reference genome supported similar conclusions, further supporting RAD-seq as a method that can be efficiently applied to species lacking existing genomic resources. We discuss the utility of RAD-seq approaches in burgeoning Nematostella research as well as in other cnidarian species, particularly corals, to determine phylogeographic relationships of populations and identify regions of the genome undergoing selection.
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影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
影响因子：
4.5
作者：
de Koning AP;Gu W;Castoe TA;Batzer MA;Pollock DD
通讯作者：
Pollock DD
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
3.5
作者：
Botsford, L. W.;White, J. W.;Coffroth, M. -A.;Paris, C. B.;Planes, S.;Shearer, T. L.;Thorrold, S. R.;Jones, G. P.
通讯作者：
Jones, G. P.
一个独特的水平基因转移事件为八角形的线粒体基因组提供了活跃的不匹配修复基因，该基因具有异常的独立功能。
影响因子：
3.4
作者：
Bilewitch JP;Degnan SM
通讯作者：
Degnan SM