Koot Emily, Wu Chen, Ruza Igor, Hilario Elena, Storey Roy, Wells Richard, Chagné David, Wellenreuther Maren
The New Zealand Institute for Plant and Food Research Ltd Palmerston North New Zealand.
The New Zealand Institute for Plant and Food Research Ltd Auckland New Zealand.
Evol Appl. 2021 Nov 23;14(12):2848-2863. doi: 10.1111/eva.13317. eCollection 2021 Dec.
The assessment of the genetic structuring of biodiversity is crucial for management and conservation. This is particularly critical for widely distributed and highly mobile deep-water teleosts, such as hoki (). This species is significant to Māori people and supports the largest commercial fishery in New Zealand, but uncertainty about its stock structure presents a challenge for management. Here, we apply a comprehensive genomic analysis to shed light on the demographic structure of this species by (1) assembling the genome, (2) generating a catalogue of genome-wide SNPs to infer the stock structure and (3) identifying regions of the genome under selection. The final genome assembly used short and long reads and is near complete, representing 93.8% of BUSCO genes, and consisting of 566 contigs totalling 501 Mb. Whole-genome re-sequencing of 510 hoki sampled from 14 locations around New Zealand and Australia, at a read depth greater than 10×, produced 227,490 filtered SNPs. Analyses of these SNPs were able to resolve the stock structure of hoki into two genetically and geographically distinct clusters, one including the Australian and the other one all New Zealand locations, indicating genetic exchange between these regions is limited. Location differences within New Zealand samples were much more subtle (global = 0.0006), and while small and significant differences could be detected, they did not conclusively identify additional substructures. Ten putative adaptive SNPs were detected within the New Zealand samples, but these also did not geographically partition the dataset further. Contemporary and historical estimation suggest the current New Zealand population of hoki is large yet declining. Overall, our study provides the first genomic resources for hoki and provides detailed insights into the fine-scale population genetic structure to inform the management of this species.
生物多样性遗传结构的评估对于管理和保护至关重要。这对于广泛分布且高度洄游的深水硬骨鱼来说尤为关键，比如无须鳕（hoki）。该物种对毛利人意义重大，并且支撑着新西兰最大的商业渔业，但关于其种群结构的不确定性给管理带来了挑战。在此，我们应用全面的基因组分析来阐明该物种的种群结构，具体做法包括：（1）组装基因组；（2）生成全基因组单核苷酸多态性（SNP）目录以推断种群结构；（3）识别受选择的基因组区域。最终的基因组组装使用了短读长和长读长数据，近乎完整，代表了93.8%的脊椎动物单拷贝直系同源基因（BUSCO基因），由566个重叠群组成，总计501兆碱基。对从新西兰和澳大利亚各地14个地点采集的510条无须鳕进行全基因组重测序，测序深度大于10倍，产生了227,490个经过筛选的SNP。对这些SNP的分析能够将无须鳕的种群结构解析为两个在遗传和地理上截然不同的群体，一个包括澳大利亚的样本，另一个包括所有新西兰的样本，这表明这些区域之间的基因交流有限。新西兰样本内部的地点差异更为细微（全局FST = 0.0006），虽然能够检测到微小但显著的差异，但这些差异并未明确识别出其他亚结构。在新西兰样本中检测到了10个假定的适应性SNP，但这些SNP也没有在地理上进一步划分数据集。当代和历史有效种群大小估计表明，新西兰目前的无须鳕种群数量庞大但正在减少。总体而言，我们的研究为无须鳕提供了首个基因组资源，并对精细尺度的种群遗传结构提供了详细见解，为该物种的管理提供了依据。
