Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.
Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.
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DOI：
10.1186/1471-2164-15-1060
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发表时间：
2014-12-11
期刊：
影响因子：
4.4
通讯作者：
Griffin DK
中科院分区：
文献类型：
--
作者：
Romanov MN;Farré M;Lithgow PE;Fowler KE;Skinner BM;O'Connor R;Fonseka G;Backström N;Matsuda Y;Nishida C;Houde P;Jarvis ED;Ellegren H;Burt DW;Larkin DM;Griffin DK
多种鸟类基因组序列的可用性极大地提高了我们定义整体基因组组织和重建进化变化的能力。在鸟类中，这一过程以前受到一种近乎难以处理的核型的阻碍，并且几乎完全依赖于只有最大染色体的比较分子细胞遗传学。本文分析了在交互式浏览器Evolution Highway上获得的21个鸟类基因组序列（大多数是新组装的）的新全基因组序列信息。专注于六个最佳组合的基因组使我们能够为每条染色体组装一个假定的恐龙祖先的核型。重建导致每个物种基因组组织的进化事件，我们确定斑马雀和虎皮鹦鹉的变化速度最快，与雀形目和鹦鹉形目的快速物种形成事件一致。染色体内和染色体间的变化分别用一系列倒位和易位来解释，断点重复使用是司空见惯的。在对鸡和斑胸草雀的分析中，我们发现几乎没有证据支持进化断点区域与重组热点相关的假设，但一些证据支持微染色体在大多数被分析的21种物种中很大程度上代表了保守的合性块的假设。除了一个物种外，所有物种都显示了单倍体染色体计数预测的微染色体重排的预期数量。然而，鸵鸟似乎保留了2n = 80的整体核型结构，尽管经历了大量（26）迄今未描述的染色体间变化。结果表明，存在一种机制来保持静态的整体鸟类核型/基因组结构，包括微染色体，很少发生广泛的染色体间变化（例如，在鸵鸟和虎皮鹦鹉谱系中）。在被分析的物种中，与恐龙祖先相比，鸡的血统似乎经历了最少的变化。本文的在线版本（doi:10.1186/1471-2164-15-1060）包含补充材料，可供授权用户使用。
The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species’ genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor. The online version of this article (doi:10.1186/1471-2164-15-1060) 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：
64.8
作者：
通讯作者：
--
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.
影响因子：
7
作者：
Backstrom, Niclas;Forstmeier, Wolfgang;Ellegren, Hans
通讯作者：
Ellegren, Hans
影响因子：
3.3
作者：
FONTDEVILA, A;RUIZ, A;ALONSO, G
通讯作者：
ALONSO, G