Dense sampling of bird diversity increases power of comparative genomics.
Dense sampling of bird diversity increases power of comparative genomics.
复制标题
鸟类多样性的密集采样增强了比较基因组学的力量
DOI：
10.1038/s41586-020-2873-9
复制
发表时间：
2020-11
期刊：
影响因子：
64.8
通讯作者：
Zhang G
中科院分区：
文献类型：
--
作者：
Feng S;Stiller J;Deng Y;Armstrong J;Fang Q;Reeve AH;Xie D;Chen G;Guo C;Faircloth BC;Petersen B;Wang Z;Zhou Q;Diekhans M;Chen W;Andreu-Sánchez S;Margaryan A;Howard JT;Parent C;Pacheco G;Sinding MS;Puetz L;Cavill E;Ribeiro ÂM;Eckhart L;Fjeldså J;Hosner PA;Brumfield RT;Christidis L;Bertelsen MF;Sicheritz-Ponten T;Tietze DT;Robertson BC;Song G;Borgia G;Claramunt S;Lovette IJ;Cowen SJ;Njoroge P;Dumbacher JP;Ryder OA;Fuchs J;Bunce M;Burt DW;Cracraft J;Meng G;Hackett SJ;Ryan PG;Jønsson KA;Jamieson IG;da Fonseca RR;Braun EL;Houde P;Mirarab S;Suh A;Hansson B;Ponnikas S;Sigeman H;Stervander M;Frandsen PB;van der Zwan H;van der Sluis R;Visser C;Balakrishnan CN;Clark AG;Fitzpatrick JW;Bowman R;Chen N;Cloutier A;Sackton TB;Edwards SV;Foote DJ;Shakya SB;Sheldon FH;Vignal A;Soares AER;Shapiro B;González-Solís J;Ferrer-Obiol J;Rozas J;Riutort M;Tigano A;Friesen V;Dalén L;Urrutia AO;Székely T;Liu Y;Campana MG;Corvelo A;Fleischer RC;Rutherford KM;Gemmell NJ;Dussex N;Mouritsen H;Thiele N;Delmore K;Liedvogel M;Franke A;Hoeppner MP;Krone O;Fudickar AM;Milá B;Ketterson ED;Fidler AE;Friis G;Parody-Merino ÁM;Battley PF;Cox MP;Lima NCB;Prosdocimi F;Parchman TL;Schlinger BA;Loiselle BA;Blake JG;Lim HC;Day LB;Fuxjager MJ;Baldwin MW;Braun MJ;Wirthlin M;Dikow RB;Ryder TB;Camenisch G;Keller LF;DaCosta JM;Hauber ME;Louder MIM;Witt CC;McGuire JA;Mudge J;Megna LC;Carling MD;Wang B;Taylor SA;Del-Rio G;Aleixo A;Vasconcelos ATR;Mello CV;Weir JT;Haussler D;Li Q;Yang H;Wang J;Lei F;Rahbek C;Gilbert MTP;Graves GR;Jarvis ED;Paten B;Zhang G
全基因组测序项目正在越来越多地填充生命之树，并表征生物多样性。稀疏分类单元采样以前曾被提出混淆系统发育推断，并捕获只有一小部分的基因组多样性。在这里，我们报告了一个实质性的一步，通过分析来自92.4%的鸟类家族的363个基因组，包括267个新测序的基因组的鸟类10,000基因组（B10 K）项目的第二阶段产生的密集表示鸟类的系统发育和分子多样性。我们使用这个比较基因组数据集与管道相结合，该管道利用无参考的全基因组比对来识别比以前可能的数量更多的正向区域，并识别特定鸟类谱系中的基因组新颖性。密集采样的比对提供了一个单碱基对的选择图，使被确信预测为保守的碱基比例增加了一倍以上，并揭示了主要非编码DNA中弱选择的广泛模式。我们的研究结果表明，增加比较研究中使用的基因组的多样性可以揭示更多的共享和谱系特异性变异，并改善基因组特征的调查。我们预计，这一基因组资源将提供新的视角进化过程中的跨物种比较分析，并协助努力保护物种。来自鸟类10，000基因组计划的363个物种的基因组数据集显示出检测共享和谱系特异性变异的能力增加，证明了全基因组测序中遗传多样性分类单元采样的重要性。
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity. Sparse taxon sampling has previously been proposed to confound phylogenetic inference, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
登录
查看更多内容
10KP：系统多样性基因组测序计划。
影响因子：
9.2
作者：
Cheng S;Melkonian M;Smith SA;Brockington S;Archibald JM;Delaux PM;Li FW;Melkonian B;Mavrodiev EV;Sun W;Fu Y;Yang H;Soltis DE;Graham SW;Soltis PS;Liu X;Xu X;Wong GK
通讯作者：
Wong GK
影响因子：
64.8
作者：
Armstrong J;Hickey G;Diekhans M;Fiddes IT;Novak AM;Deran A;Fang Q;Xie D;Feng S;Stiller J;Genereux D;Johnson J;Marinescu VD;Alföldi J;Harris RS;Lindblad-Toh K;Haussler D;Karlsson E;Jarvis ED;Zhang G;Paten B
通讯作者：
Paten B
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM
影响因子：
30.8
作者：
Drake, JA;Bird, C;Hirschhorn, JN
通讯作者：
Hirschhorn, JN