The structural variation landscape in 492 Atlantic salmon genomes.
The structural variation landscape in 492 Atlantic salmon genomes.
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492个大西洋鲑鱼基因组的结构变异景观。
DOI：
10.1038/s41467-020-18972-x
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发表时间：
2020-10-14
影响因子：
16.6
通讯作者：
Macqueen DJ
中科院分区：
文献类型：
--
作者：
Bertolotti AC;Layer RM;Gundappa MK;Gallagher MD;Pehlivanoglu E;Nome T;Robledo D;Kent MP;Røsæg LL;Holen MM;Mulugeta TD;Ashton TJ;Hindar K;Sægrov H;Florø-Larsen B;Erkinaro J;Primmer CR;Bernatchez L;Martin SAM;Johnston IA;Sandve SR;Lien S;Macqueen DJ
结构变异（SV）是遗传和表型变异的主要来源，但准确分型仍然具有挑战性，因此在大多数物种中的特征很差。我们提出了一种使用全基因组测序在非模式物种中发现可靠SV的方法，并报告了492条大西洋鲑鱼（萨尔莫萨拉L.）中的15，483个高置信度SV从广泛的地理分布中取样。这些SV恢复人口的遗传结构与高分辨率，包括一个活跃的DNA转座子，广泛影响功能的特点，并重叠更多的重复基因保留从祖先鲑鱼同源四倍化事件比预期的。野生和养殖鱼类之间SV等位基因频率的变化表明驯化过程中对行为特征的多基因选择，目标是与人类神经系统疾病相关的脑表达突触网络。这项研究提供了新的见解SV在基因组进化和驯化性状的遗传结构中的作用，沿着资源支持可靠的SV发现在非模式物种。这项研究提出并验证了一种新的方法，使用全基因组测序可靠地识别非模型基因组中的结构变异（SV），该方法用于检测492条大西洋鲑鱼中的15，483个SV，揭示了它们在基因组进化和驯化遗传结构中的作用。
Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species. This study presents and validates a novel approach to reliably identify structural variations (SVs) in non-model genomes using whole genome sequencing, which was used to detect 15,483 SVs in 492 Atlantic salmon, shedding light on their roles in genome evolution and the genetic architecture of domestication.
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影响因子：
16.6
作者：
Berthelot, Camille;Brunet, Frederic;Chalopin, Domitille;Juanchich, Amelie;Bernard, Maria;Noel, Benjamin;Bento, Pascal;Da Silva, Corinne;Labadie, Karine;Alberti, Adriana;Aury, Jean-Marc;Louis, Alexandra;Dehais, Patrice;Bardou, Philippe;Montfort, Jerome;Klopp, Christophe;Cabau, Cedric;Gaspin, Christine;Thorgaard, Gary H.;Boussaha, Mekki;Quillet, Edwige;Guyomard, Rene;Galiana, Delphine;Bobe, Julien;Volff, Jean-Nicolas;Genet, Carine;Wincker, Patrick;Jaillon, Olivier;Roest Crollius, Hugues;Guiguen, Yann
通讯作者：
Guiguen, Yann
影响因子：
10.7
作者：
Minh BQ;Nguyen MA;von Haeseler A
通讯作者：
von Haeseler A
影响因子：
6.8
作者：
Dachtler J;Glasper J;Cohen RN;Ivorra JL;Swiffen DJ;Jackson AJ;Harte MK;Rodgers RJ;Clapcote SJ
通讯作者：
Clapcote SJ
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：
12.3
作者：
Becker, Timothy;Lee, Wan-Ping;Malhotra, Ankit
通讯作者：
Malhotra, Ankit