The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly.
The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly.
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DOI：
10.1371/journal.pone.0204076
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Koop BF
中科院分区：
文献类型：
--
作者：
Christensen KA;Rondeau EB;Minkley DR;Leong JS;Nugent CM;Danzmann RG;Ferguson MM;Stadnik A;Devlin RH;Muzzerall R;Edwards M;Davidson WS;Koop BF
北极红点鲑有一个环极分布，坚持在极端的环境条件下，并达到年龄未知的大多数其他鲑鱼。红点鲑属主要由基因组结构比姐妹属的大多数虹鳟属和萨尔莫物种更像祖先鲑鱼基因组的物种组成。据认为，基因组的这一方面可能是重要的地方适应（由于增加重组）和anadromy（鱼类从咸水到淡水的迁移）。在这项研究中，我们描述了一个新的遗传图谱的生成，测序和组装的北极红点鲑基因组（GenBank登录号：GCF_002910315.2）使用新创建的遗传图谱和以前的遗传图谱，并提出了几个分析的北极红点鲑基因和基因组组装。新生成的遗传图谱由8，574个独特的遗传标记组成，除了三个主要的结构差异外，与以前的遗传图谱相似。北极红点鲑组装基因组的N50、确定的BUSCO、重复DNA含量和总大小都与其他组装的鲑鱼基因组相当。一项鉴定直向同源基因的分析显示，在鲑鱼科鱼类之间可以鉴定出大量的直向同源基因，并且许多物种之间似乎具有高度保守的基因表达谱。比较直向同源基因的表达谱可以让我们更好地了解哪些基因更可能影响物种特异性表型。
Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes.
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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：
2.4
作者：
BERNATCHEZ, L;GLEMET, H;DANZMANN, RG
通讯作者：
DANZMANN, RG
影响因子：
2.9
作者：
Brännäs, E;Linnér, J
通讯作者：
Linnér, J
影响因子：
3.7
作者：
Christensen KA;Leong JS;Sakhrani D;Biagi CA;Minkley DR;Withler RE;Rondeau EB;Koop BF;Devlin RH
通讯作者：
Devlin RH
影响因子：
3.3
作者：
Castric, V;Bonney, F;Bernatchez, L
通讯作者：
Bernatchez, L