Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856.
Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856.
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DOI：
10.1534/genetics.115.175950
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发表时间：
2015-07
期刊：
影响因子：
3.3
通讯作者：
Waterston RH
中科院分区：
文献类型：
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作者：
Thompson OA;Snoek LB;Nijveen H;Sterken MG;Volkers RJ;Brenchley R;Van't Hof A;Bevers RP;Cossins AR;Yanai I;Hajnal A;Schmid T;Perkins JD;Spencer D;Kruglyak L;Andersen EC;Moerman DG;Hillier LW;Kammenga JE;Waterston RH
秀丽隐杆线虫的夏威夷株(CB4856)是与典型的实验室株N2最不同的菌株之一，已被广泛应用于发育、种群和进化研究。为了提高菌株的实用性，我们利用了各种资源和策略，生成了CB4856基因组的草稿序列。与参考的N2序列相比，CB4856基因组有327,050个单核苷酸变异(SNV)和79,529个插入-缺失事件，导致CB4856中总共缺失3.3Mb的N2序列和CB4856中存在但不存在的1.4Mb的序列。正如以前报道的那样，SNV的密度在染色体上是不同的，染色体臂的平均变异比中心大。此外，我们还发现了61个区域，共2.8Mb，分布在所有六条染色体上，SNV密度显著升高，SNV从2%到16%不等。对其他野生分离株的调查显示，每个地区的两种可供选择的单倍型分布广泛，这表明它们是通过长期进化过程中的平衡选择来保持的。这些不同的区域包含大量来自快速进化的大家族的基因，编码F-box、MATH、Bath、七个跨膜G偶联受体和核激素受体，这表明它们在自然环境中提供了选择优势。该序列草案提供了CB4856和N2菌株之间序列差异的全面目录，这将有助于分子解剖它们的表型差异。我们的工作还强调了在评估基因组之间的差异时超越简单的读数与参考基因组的比对的重要性。
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population, and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. When compared against the N2 reference, the CB4856 genome has 327,050 single nucleotide variants (SNVs) and 79,529 insertion–deletion events that result in a total of 3.3 Mb of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 but not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, which have a greatly elevated SNV density, ranging from 2 to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors, suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.