Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes.
Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes.
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DOI：
10.1186/s13059-018-1544-8
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发表时间：
2018-10-05
期刊：
影响因子：
12.3
通讯作者：
Larkin DM
中科院分区：
文献类型：
--
作者：
Damas J;Kim J;Farré M;Griffin DK;Larkin DM
祖先核型的重建对于我们理解基因组进化是至关重要的，它允许鉴定塑造现存基因组的总体变化。识别这些变化及其发生的时间可以揭示每个物种的生物学、进化支系及其进化史。然而，这受到大多数基因组组装的碎片性和可用软件的限制的阻碍。这些限制在鸟类中尤其明显，迄今为止只报道了10个染色体水平的组装。尽管如此，应用于片段基因组组装的算法方法可以帮助确定已定义的分类群体中染色体变化的模式。在这里，我们利用DESCHRAMBLER算法进行了鸟类祖先染色体结构和进化的第一次大规模研究。该算法使我们能够重建鸟类进化的14个关键节点的整体基因组结构，从鸟类祖先到Estrildidae， Thraupidae和Fringillidae家族的祖先。对这些重建的分析为鸟类进化过程中重排率的可变性提供了重要的见解，并允许检测与进化断点区域染色体分布相关的模式。此外，在我们的重建中包含微染色体使我们能够对这些鸟类染色体的进化提供新的见解，特别是。本文的在线版本（10.1186/s13059-018-1544-8）包含补充资料，仅供授权用户使用。
Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evolutionary history. However, this is impeded by both the fragmented nature of the majority of genome assemblies and the limitations of the available software to work with them. These limitations are particularly apparent in birds, with only 10 chromosome-level assemblies reported thus far. Algorithmic approaches applied to fragmented genome assemblies can nonetheless help define patterns of chromosomal change in defined taxonomic groups. Here, we make use of the DESCHRAMBLER algorithm to perform the first large-scale study of ancestral chromosome structure and evolution in birds. This algorithm allows us to reconstruct the overall genome structure of 14 key nodes of avian evolution from the Avian ancestor to the ancestor of the Estrildidae, Thraupidae and Fringillidae families. Analysis of these reconstructions provides important insights into the variability of rearrangement rates during avian evolution and allows the detection of patterns related to the chromosome distribution of evolutionary breakpoint regions. Moreover, the inclusion of microchromosomes in our reconstructions allows us to provide novel insights into the evolution of these avian chromosomes, specifically. The online version of this article (10.1186/s13059-018-1544-8) contains supplementary material, which is available to authorized users.
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DOI：
10.1126/science.1253451
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jarvis ED;Mirarab S;Aberer AJ;Li B;Houde P;Li C;Ho SY;Faircloth BC;Nabholz B;Howard JT;Suh A;Weber CC;da Fonseca RR;Li J;Zhang F;Li H;Zhou L;Narula N;Liu L;Ganapathy G;Boussau B;Bayzid MS;Zavidovych V;Subramanian S;Gabaldón T;Capella-Gutiérrez S;Huerta-Cepas J;Rekepalli B;Munch K;Schierup M;Lindow B;Warren WC;Ray D;Green RE;Bruford MW;Zhan X;Dixon A;Li S;Li N;Huang Y;Derryberry EP;Bertelsen MF;Sheldon FH;Brumfield RT;Mello CV;Lovell PV;Wirthlin M;Schneider MP;Prosdocimi F;Samaniego JA;Vargas Velazquez AM;Alfaro-Núñez A;Campos PF;Petersen B;Sicheritz-Ponten T;Pas A;Bailey T;Scofield P;Bunce M;Lambert DM;Zhou Q;Perelman P;Driskell AC;Shapiro B;Xiong Z;Zeng Y;Liu S;Li Z;Liu B;Wu K;Xiao J;Yinqi X;Zheng Q;Zhang Y;Yang H;Wang J;Smeds L;Rheindt FE;Braun M;Fjeldsa J;Orlando L;Barker FK;Jønsson KA;Johnson W;Koepfli KP;O'Brien S;Haussler D;Ryder OA;Rahbek C;Willerslev E;Graves GR;Glenn TC;McCormack J;Burt D;Ellegren H;Alström P;Edwards SV;Stamatakis A;Mindell DP;Cracraft J;Braun EL;Warnow T;Jun W;Gilbert MT;Zhang G
通讯作者：
Zhang G
影响因子：
12.3
作者：
Cai Q;Qian X;Lang Y;Luo Y;Xu J;Pan S;Hui Y;Gou C;Cai Y;Hao M;Zhao J;Wang S;Wang Z;Zhang X;He R;Liu J;Luo L;Li Y;Wang J
通讯作者：
Wang J
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
4.4
作者：
Gallardo, M. H.;Gonzalez, C. A.;Cebrian, I.
通讯作者：
Cebrian, I.
影响因子：
1.7
作者：
Griffin, D. K.;Robertson, L. B. W.;Skinner, B. M.
通讯作者：
Skinner, B. M.