The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for North American Atlantic salmon
The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for North American Atlantic salmon
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北美大西洋鲑鱼第一个染色体水平从头基因组组装的产生以及 50K SNP 阵列的开发和验证
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发表时间：
2022
期刊：
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通讯作者：
Y. Palti
中科院分区：
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作者：
Guangtu Gao;G. Waldbieser;R. Youngblood;Dongyan Zhao;M. Pietrak;M. Allen;J. Stannard;John Buchanan;Roseanna L. Long;Melissa Milligan;Gary Burr;Katherine Mejia;Moira J. Sheehan;B. Scheffler;C. Rexroad;B. Peterson;Y. Palti
鉴于起源于欧洲的大西洋三文鱼和北美(N.A.)之间的遗传和基因组差异在起源上，为每个谱系开发独特的基因组资源是至关重要的。在这里，我们描述了我们最近开发的用于北大西洋鲑鱼基因组和遗传研究的资源。首先，利用80个大西洋鲑鱼个体的全基因组测序数据构建了一个新的包含310万个SNP的大西洋鲑鱼单核苷酸多态(SNP)数据库；其次，开发并验证了一个高密度的50K SNP阵列，该阵列丰富了基因组的基因区域，包含3个性别决定标记和61个大陆来源标记；第三，从141个全同胞家庭的2512个个体中获得了由27个连锁组和36K SNP标记组成的遗传图谱；最后，利用PacBio长阅读构建了雄性N.A.大西洋鲑鱼基因组的染色体水平去新组装。来自Hi-C邻近连接序列和Bionano光学作图的信息被用来将重叠群连接成支架。该组件包含1755个脚手架和1253个间隙，总长度为2.83 GB，N50为17.2Mb。经BUSCO分析，发现该集合中96.2%的保守放线鸟基因，并利用遗传连锁信息指导27条染色体序列的形成。相比之下，欧洲大西洋鲑鱼谱系的核型由29条染色体组成。与欧洲大西洋鲑鱼参考基因组组合的比较分析证实，这两个品系之间的核型差异是由于染色体Ssa01的一个分裂以及染色体Ssa01的p臂与Ssa23、Ssa08与Ssa29和Ssa26与Ssa28的三条染色体融合造成的。我们为大西洋鲑鱼创造的基因组资源为遗传研究和管理这种高度珍贵的物种的养殖和野生种群提供了至关重要的推动。
Given the genetic and genomic differences between Atlantic salmon of European origin and North American (N.A.) origin, it is crucial to develop unique genomic resources for each lineage. Here we describe the resources that we recently developed for genomic and genetic research in N.A. Atlantic salmon. Firstly, a new single nucleotide polymorphism (SNP) database for N.A. Atlantic salmon consisting of 3.1 million putative SNPs was generated using data from whole genome resequencing of 80 N.A. Atlantic salmon individuals; Secondly, a high density 50K SNP array enriched for the genic regions of the genome and containing three sex determination and 61 continent of origin markers was developed and validated; Thirdly, a genetic map composed of 27 linkage groups with 36K SNP markers, was generated from 2,512 individuals in 141 full-sib families; Finally, a chromosome level de-novo assembly of a male N.A. Atlantic salmon genome was generated using PacBio long-reads. Information from Hi-C proximity ligation sequences and Bionano optical mapping was used to concatenate the contigs into scaffolds. The assembly contains 1,755 scaffolds and only 1,253 gaps, with a total length of 2.83 Gb and N50 of 17.2 Mb. A BUSCO analysis detected 96.2% of conserved Actinopterygii genes in the assembly and the genetic linkage information was used to guide the formation of 27 chromosome sequences. In contrast, the karyotype of the European Atlantic salmon lineage is composed of 29 chromosomes. Comparative analysis with the reference genome assembly of the European Atlantic salmon confirmed that the karyotype differences between the two linages are caused by a fission in chromosome Ssa01 and three chromosome fusions including the p arm of chromosome Ssa01 with Ssa23, Ssa08 with Ssa29 and Ssa26 with Ssa28. The genomic resources we have generated for Atlantic salmon provide a crucial boost for genetic research and for management of farmed and wild populations in this highly valued species.