Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.
Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.
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DOI：
10.1101/gr.171546.113
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发表时间：
2014-07
期刊：
影响因子：
7
通讯作者：
Mackay TF
中科院分区：
文献类型：
--
作者：
Huang W;Massouras A;Inoue Y;Peiffer J;Ràmia M;Tarone AM;Turlapati L;Zichner T;Zhu D;Lyman RF;Magwire MM;Blankenburg K;Carbone MA;Chang K;Ellis LL;Fernandez S;Han Y;Highnam G;Hjelmen CE;Jack JR;Javaid M;Jayaseelan J;Kalra D;Lee S;Lewis L;Munidasa M;Ongeri F;Patel S;Perales L;Perez A;Pu L;Rollmann SM;Ruth R;Saada N;Warner C;Williams A;Wu YQ;Yamamoto A;Zhang Y;Zhu Y;Anholt RR;Korbel JO;Mittelman D;Muzny DM;Gibbs RA;Barbadilla A;Johnston JS;Stone EA;Richards S;Deplancke B;Mackay TF
果蝇遗传参考小组(DGRP)是一个包含205个测序近交系的社区资源，旨在提高我们对自然发生的遗传变异对分子和生物表型的影响的理解。我们使用综合基因分型策略识别了4,853,802个单核苷酸多态(SNPs)和1,296,080个非SNP变异体。我们的分子群体基因组分析显示，缺失比插入突变率更高，对缺失的纯化选择更强。对插入的选择弱于对缺失的选择，这与我们观察到的由流式细胞术确定的基因组大小分布一致，这是向更大的基因组倾斜的。插入/缺失和单核苷酸多态之间以及与局部重组呈正相关，提示它们的非随机性分布与搭便车和背景选择有关。我们的细胞遗传学分析确定了DGRP中的16个多态倒位。常见的倒置核型和标准核型在遗传上是不同的，并解释了DGRP系之间亲缘关系的大部分差异。有趣的是，基因组大小和许多数量性状的变异与倒置密切相关。大约50%的DGRP品系感染了Wolbachia，有4个品系含有Wolbachia序列的种系插入，但Wolbachia感染对数量性状的影响很小。DGRP是对果蝇基因组进行功能注释的持续努力的补充。事实上，15%的黑腹果蝇基因分离了DGRP中潜在受损的蛋白质，对数量性状的全基因组分析确定了新的候选基因。DGRP品系、序列数据、基因类型、质量分数、表型以及分析和可视化工具都是公开可用的。
The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.
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影响因子：
64.8
作者：
Clark, Andrew G.;Eisen, Michael B.;MacCallum, Iain
通讯作者：
MacCallum, Iain
影响因子：
64.8
作者：
Gan X;Stegle O;Behr J;Steffen JG;Drewe P;Hildebrand KL;Lyngsoe R;Schultheiss SJ;Osborne EJ;Sreedharan VT;Kahles A;Bohnert R;Jean G;Derwent P;Kersey P;Belfield EJ;Harberd NP;Kemen E;Toomajian C;Kover PX;Clark RM;Rätsch G;Mott R
通讯作者：
Mott R
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
3.1
作者：
Bridges, CB
通讯作者：
Bridges, CB
影响因子：
4.5
作者：
Corbett-Detig, Russell B.;Hartl, Daniel L.
通讯作者：
Hartl, Daniel L.