[论文解读] Assembly ASM291031v2 (Genbank: GCA_002910315.2) identified as assembly of the Northern Dolly Varden (Salvelinus malma malma) genome, and not the Arctic char (S. alpinus) genome

S. V. Shedko|arXiv (Cornell University)|Dec 5, 2019

Identification and Quantification in Food被引用 4

一句话总结

本研究确定基因组组装ASM291031v2（GenBank: GCA_002910315.2）源自北方多莉鳟（Salvelinus malma malma），而非先前假设的北极茴鱼（S. alpinus）。尽管存在先前的误解，但通过线粒体DNA（线粒体基因组）和核基因标记（ITS1、RAG1、SFO-12、SFO-18、SMM-21）分析，确认雌性IW2-2015样本属于BERING单倍群，并与北方多莉鳟共享诊断等位基因，表明原始测序项目中存在标签错误。

ABSTRACT

To date, twelve complete genomes representing eleven species belonging to six genera have been sequenced in salmonids. For the genus Salvelinus, it was supposed to sequence the genome of Arctic char, one of the most variable species of vertebrate animals. Sequencing was carried out (Christensen et al., 2018) using the tissues of the female IW2-2015 obtained from the company engaged in industrial aquaculture of chars - Icy Waters Ltd. The company exploits two of its own broodstocks - NL and TR, originating from the chars from the Nauyuk Lake and the Tree River (Nunavut, Canada). Since the complete mitochondrial genome of the female IW2-2015 was absent in the published assembly ASM291031v2, we determined its type and complete sequence from the sequence read archives taken from Genbank. It was found that the female's mitogenome belongs to the BERING haplogroup, which is characteristic of Northern Dolly Varden S. malma malma. Analysis of other unlinked diagnostic loci encoded by nuclear DNA (ITS1, RAG1, SFO-12, SFO-18, SMM-21) also revealed distinctive characters of Northern Dolly Varden in female IW2-2015. It was concluded that the genomic assembly ASM291031v2 was obtained not from an individual of Arctic char S. alpinus, but from an individual of a related species - Northern Dolly Varden S. malma malma. The identical to the IW2-2015 female characteristics of diagnostic loci were found in other individuals from the broodstock TR. Apparently, the broodstock TR is entirely a strain derived from Northern Dolly Varden. Since assembly ASM291031v2 was obtained from a specimen originated from the marginal population of Northern Dolly Varden (Tree R.) isolated from the main range of the species and with some traces of introgressive hybridization, this assembly can hardly be considered as a description of a typical genome of S. malma malma.

研究动机与目标

• 解决基因组组装ASM291031v2的分类学身份问题，该组装此前被假设源自北极茴鱼（S. alpinus）。
• 确定用于测序项目的雌性IW2-2015个体的真实物种来源。
• 评估该样本来源的亲鱼群TR是否在遗传上与北方多莉鳟一致，而非北极茴鱼。
• 纠正科学记录中关于此广泛使用的鲑科基因组组装物种命名的问题。

提出的方法

• 从GenBank中的SRA数据中测序并分析了雌性IW2-2015的完整线粒体基因组，因其在原始组装中缺失。
• 将线粒体基因组序列与已知单倍群进行比较，确认其属于北方多莉鳟特有的BERING单倍群。
• 分析了未连锁的核DNA标记（ITS1、RAG1、SFO-12、SFO-18、SMM-21），以鉴定与Salvelinus malma malma特异相关的诊断等位基因。
• 将IW2-2015个体的遗传谱型与TR亲鱼群中其他个体的谱型进行交叉比对，以评估谱系一致性。
• 评估了在孤立的Tree River种群中是否存在渐渗杂交，以解释遗传分化。

实验结果

研究问题

• RQ1 基因组组装ASM291031v2是否正确归类为北极茴鱼（S. alpinus），还是存在标签错误？
• RQ2 用于测序项目的雌性IW2-2015个体的真实物种身份是什么？
• RQ3 IW2-2015样本的线粒体和核基因标记是否与北方多莉鳟（S. malma malma）的特征一致？
• RQ4 该样本来源的TR亲鱼群是否在遗传上与北方多莉鳟一致，而非北极茴鱼？
• RQ5 在孤立的Tree River种群中，渐渗杂交在多大程度上影响了ASM291031v2组装的基因组身份？

主要发现

• 通过SRA数据确定了雌性IW2-2015的完整线粒体基因组，并发现其属于BERING单倍群，这是北方多莉鳟（S. malma malma）的标志性特征。
• IW2-2015个体中的核DNA标记（ITS1、RAG1、SFO-12、SFO-18、SMM-21）显示出与北方多莉鳟一致的诊断等位基因，而非北极茴鱼。
• TR亲鱼群与IW2-2015雌性个体表现出完全相同的诊断等位基因，表明其完全源自北方多莉鳟。
• 因此，基因组组装ASM291031v2并非来自北极茴鱼（S. alpinus），而是来自北方多莉鳟（S. malma malma）。
• 该样本源自努纳武特省Tree River的北方多莉鳟边缘种群，存在低水平渐渗杂交的证据。
• 由于其孤立且可能已杂交的谱系，ASM291031v2组装不能被视为典型S. malma malma的代表性基因组。