Genome-wide fine-scale recombination rate variation in Drosophila melanogaster.
Genome-wide fine-scale recombination rate variation in Drosophila melanogaster.
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DOI：
10.1371/journal.pgen.1003090
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Song YS
中科院分区：
文献类型：
--
作者：
Chan AH;Jenkins PA;Song YS
从群体基因组数据中估计果蝇的精细重组图是一个具有挑战性的问题，特别是因为背景重组率很高。在本文中，一个新的计算方法来解决这一挑战。通过广泛的模拟研究，它表明，该方法允许更准确的推理，并表现出更大的鲁棒性的自然选择和噪声的影响，相比，一个良好的使用以前的方法开发的研究精细规模的重组率在人类基因组中的变化。作为一个应用，全基因组的遗传变异数据进行分析的两个果蝇种群，一个来自北美（罗利，美国）和非洲（Gikongoro，卢旺达）。结果表明，精细尺度的复合率变化在整个D。黑腹果蝇基因组，在所有染色体和两个种群。在精细尺度上，保守的，系统的搜索重组热点的证据表明存在少数推定的热点，每个热点的强度至少增加了十倍以上的背景速率。小波分析进行比较估计的重组地图在两个人口和量化的程度，重组率是保守的。一般来说，在非常广泛的尺度上观察到相似性，但在精细尺度上观察到实质性差异。X染色体的平均重组率似乎高于两个种群中常染色体的平均重组率，并且这种模式在非洲种群中比北美种群更明显。利用小波分析研究了各种基因组特征之间的相关性，包括重组率，多样性，分歧，GC含量，基因含量和序列质量，结果表明，最显着的差异D。黑腹动物和人类的关系是重组和多样性之间的关系。减数分裂是染色体在减数分裂期间交换遗传物质的过程。它在进化中很重要，因为它为后代提供了新的基因组合，因此估计重组率在各种群体基因组推断问题中具有根本的重要性。在本文中，我们开发了一种新的统计方法，使强大的估计果蝇，常见的果蝇属，其中的背景重组率高，自然选择一直盛行的精细尺度重组图谱。我们应用我们的方法来产生一个北美人口和非洲人口的D。黑腹果蝇对于这两个群体，我们发现广泛的重组率在整个基因组的精细尺度的变化。我们提供了一个定量表征的相似性和差异之间的重组图的两个人口，我们的研究揭示了高相关性在广泛的规模和低相关性在精细的尺度，已被记录在人群中。我们还研究了各种基因组特征之间的相关性。此外，使用保守的方法，我们找到了一些假定的重组“热点”区域与坚实的统计支持的本地海拔至少10倍的背景重组率。
Estimating fine-scale recombination maps of Drosophila from population genomic data is a challenging problem, in particular because of the high background recombination rate. In this paper, a new computational method is developed to address this challenge. Through an extensive simulation study, it is demonstrated that the method allows more accurate inference, and exhibits greater robustness to the effects of natural selection and noise, compared to a well-used previous method developed for studying fine-scale recombination rate variation in the human genome. As an application, a genome-wide analysis of genetic variation data is performed for two Drosophila melanogaster populations, one from North America (Raleigh, USA) and the other from Africa (Gikongoro, Rwanda). It is shown that fine-scale recombination rate variation is widespread throughout the D. melanogaster genome, across all chromosomes and in both populations. At the fine-scale, a conservative, systematic search for evidence of recombination hotspots suggests the existence of a handful of putative hotspots each with at least a tenfold increase in intensity over the background rate. A wavelet analysis is carried out to compare the estimated recombination maps in the two populations and to quantify the extent to which recombination rates are conserved. In general, similarity is observed at very broad scales, but substantial differences are seen at fine scales. The average recombination rate of the X chromosome appears to be higher than that of the autosomes in both populations, and this pattern is much more pronounced in the African population than the North American population. The correlation between various genomic features—including recombination rates, diversity, divergence, GC content, gene content, and sequence quality—is examined using the wavelet analysis, and it is shown that the most notable difference between D. melanogaster and humans is in the correlation between recombination and diversity. Recombination is a process by which chromosomes exchange genetic material during meiosis. It is important in evolution because it provides offspring with new combinations of genes, and so estimating the rate of recombination is of fundamental importance in various population genomic inference problems. In this paper, we develop a new statistical method to enable robust estimation of fine-scale recombination maps of Drosophila, a genus of common fruit flies, in which the background recombination rate is high and natural selection has been prevalent. We apply our method to produce fine-scale recombination maps for a North American population and an African population of D. melanogaster. For both populations, we find extensive fine-scale variation in recombination rate throughout the genome. We provide a quantitative characterization of the similarities and differences between the recombination maps of the two populations; our study reveals high correlation at broad scales and low correlation at fine scales, as has been documented among human populations. We also examine the correlation between various genomic features. Furthermore, using a conservative approach, we find a handful of putative recombination “hotspot” regions with solid statistical support for a local elevation of at least 10 times the background recombination rate.
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影响因子：
1.2
作者：
Bhaskar A;Kamm JA;Song YS
通讯作者：
Song YS
影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
9.8
作者：
Fearnhead, P;Smith, NGC
通讯作者：
Smith, NGC
影响因子：
30.8
作者：
通讯作者：
--
种群基因组学：果蝇果蝇中多态性和差异的全基因组分析。
影响因子：
9.8
作者：
Begun, David J.;Holloway, Alisha K.;Stevens, Kristian;Hillier, LaDeana W.;Poh, Yu-Ping;Hahn, Matthew W.;Nista, Phillip M.;Jones, Corbin D.;Kern, Andrew D.;Dewey, Colin N.;Pachter, Lior;Myers, Eugene;Langley, Charles H.
通讯作者：
Langley, Charles H.