Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK.
Collaborative Centre for Sustainable Use of the Seas, University of East Anglia, Norwich, UK.
BMC Genomics. 2024 Mar 4;25(1):233. doi: 10.1186/s12864-024-10141-4.
Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited.
A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome.
We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.
巴塔哥尼亚牙鱼（Dissostichus eleginoides）是南极鳕鱼科中一种具有重要经济和生态价值的鱼类。幼鱼随着成熟和生长而逐渐占据更深的水域，成年鱼在南大洋亚南极岛屿周围的南部大陆架和斜坡上生活，最深可达 2500 米。作为顶级掠食者，它们是食物网的关键组成部分，以各种猎物为食，包括磷虾、鱿鱼和其他鱼类。尽管它很重要，但基因组序列数据，这些数据可以用于更准确地确定巴塔哥尼亚牙鱼和南极牙鱼之间的分化时间，或者确定它是否与生活在更极地或赤道地区的鱼类具有相同的温度适应能力，到目前为止还很有限。
我们使用 Illumina、PacBio 和 Omni-C 测序技术的组合生成了高质量的 D. eleginoides 基因组。为了辅助基因组注释，还使用短读和长读测序方法从各种牙鱼组织中生成了转录组。最终的基因组组装大小为 797.8 Mb，N50 支架长度为 3.5 Mb。大约 31.7%的基因组由重复元件组成。总共鉴定出 35543 个可能的蛋白质编码区域，其中 50%已被功能注释。转录组分析表明，在所采样的组织中，约 64%的预测基因（22617 个基因）表达。比较基因组学分析表明，与南极牙鱼（Dissostichus mawsoni）的同一基因座相比，D. eleginoides 的抗冻糖蛋白（AFGP）基因座不含任何 AFGP 蛋白。这与之前研究杂交信号的研究结果一致，证实了巴塔哥尼亚牙鱼在其基因组中不具有 AFGP 编码序列。
我们已经组装并注释了巴塔哥尼亚牙鱼的基因组，这将为该物种和其他密切相关物种的生态和进化研究提供有价值的遗传资源。
