A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution.
A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution.
复制标题
DOI：
10.1111/mec.12810
复制
发表时间：
2014-08
影响因子：
4.9
通讯作者：
Ellegren H
中科院分区：
文献类型：
--
作者：
Kawakami T;Smeds L;Backström N;Husby A;Qvarnström A;Mugal CF;Olason P;Ellegren H
详细的连锁和重组率图是必要的，以充分利用基因组测序和群体基因组分析的潜力。我们使用定制的领式捕蝇器50 K SNP阵列，开发了高密度连锁图谱，其中37 262个标记被分配到33个常染色体和Z染色体的34个连锁组。最佳序图谱包含4215个标记，总距离为3132 cm，标记间平均遗传距离为0.12 cm。由于该阵列被设计为包含来自大多数支架的标记，我们获得了第二代捕蝇器基因组组装，接近完整的染色体序列（N50超级支架大小为20.2 Mb，其中1.042 Gb （1.116 Gb）锚定在染色体上，并且大部分沿染色体排列和定向）。我们发现，捕蝇草和斑胸草雀的染色体是完全同步的，但每米1.5-2.0个事件（6.6-7.5 Mb）的平均反转速率改变了染色体内的组织，这一速率足够高，反转可能参与了鸟类进化过程中的许多物种形成事件。平均重组率为3.1 cm/Mb，与染色体大小密切相关，从100 Mb以下染色体的2 cm/Mb到10 Mb以下染色体的10 cm/Mb。这种大小依赖性似乎完全是由于每条染色体的专性重组事件；如果从染色体的遗传长度中减去50厘米，则每物理单位DNA的速率在染色体上是恒定的。捕蝇草的染色体重组率与鸡的相似，但缺乏斑胸草雀染色体内部大的重组沙漠特征。
Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high-density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best-order map contained 4215 markers, with a total distance of 3132 cm and a mean genetic distance between markers of 0.12 cm. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second-generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cm/Mb and correlated closely with chromosome size, from 2 cm/Mb for chromosomes >100 Mb to >10 cm/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cm was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.
登录
查看更多内容
影响因子：
12.3
作者：
Bailey JA;Baertsch R;Kent WJ;Haussler D;Eichler EE
通讯作者：
Eichler EE
影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
影响因子：
7
作者：
Backstrom, Niclas;Forstmeier, Wolfgang;Ellegren, Hans
通讯作者：
Ellegren, Hans
影响因子：
4.9
作者：
Akesson, Mikael;Hansson, Bengt;Bensch, Staffan
通讯作者：
Bensch, Staffan
影响因子：
4.4
作者：
Aslam, Muhammad L.;Bastiaansen, John W. M.;Groenen, Martien A. M.
通讯作者：
Groenen, Martien A. M.