Chromosome-level genome assembly and annotation of the Patagonian toothfish Dissostichus eleginoides.

IF 5.8 2区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES

Scientific Data Pub Date : 2024-11-16 DOI:10.1038/s41597-024-04119-w

Seung Jae Lee, Minjoo Cho, Jinmu Kim, Eunkyung Choi, Soyun Choi, Sangdeok Chung, Jaebong Lee, Jeong-Hoon Kim, Hyun Park

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Abstract

The Patagonian toothfish (Dissostichus eleginoides) belongs to the Actinopterygii class, and the suborder Notothenioidei, which lives in cold waters in the Southern Hemisphere. We performed assembly and annotation, and we integrated the Illumina short-read sequencing for polishinng, PacBio long-read sequencing for contig-level assembly, and Hi-C sequencing technology to obtain high-quality of chromosome-level genome assembly. The final assembly analysis resulted in a total of 495 scaffolds, a genome size of 844.7 Mbp and an N50 length of 36 Mbp. Among these data, we confirmed 24 scaffolds exceeded 10 Mbp and classified as chromosome-level. The completeness of BUSCO rate was over 97%. A total gene set of 32,224 was identified. Furthermore, we analyzed the presence of AFGP genes, classified into Antarctic and sub-Antarctic categories through phylogenetic analysis. This study provides a useful resource for the genomic analysis of Patagonian toothfish and genetic insights into the comparison with Antarctic fishes.

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巴塔哥尼亚齿鱼 Dissostichus eleginoides 染色体级基因组组装与注释。

巴塔哥尼亚齿鱼（Dissostichus eleginoides）属于翼手目（Actinopterygii），齿鱼亚目（Notothenioidei），生活在南半球的寒冷水域。我们进行了组装和注释，并整合了用于抛光的Illumina短线程测序技术、用于等位基因级组装的PacBio长线程测序技术和Hi-C测序技术，以获得高质量的染色体级基因组组装。通过最终的组装分析，共得到 495 个支架，基因组大小为 844.7 Mbp，N50 长度为 36 Mbp。在这些数据中，我们确认有 24 个支架超过 10 Mbp，并将其归类为染色体级。BUSCO 的完整率超过 97%。共鉴定出 32 224 个基因集。此外，我们还分析了 AFGP 基因的存在，并通过系统发育分析将其分为南极和亚南极两类。这项研究为巴塔哥尼亚齿鱼的基因组分析提供了有用的资源，并为与南极鱼类的比较提供了遗传学见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Scientific Data Social Sciences-Education

CiteScore

11.20

自引率

4.10%

发文量

689

审稿时长

16 weeks

期刊介绍： Scientific Data is an open-access journal focused on data, publishing descriptions of research datasets and articles on data sharing across natural sciences, medicine, engineering, and social sciences. Its goal is to enhance the sharing and reuse of scientific data, encourage broader data sharing, and acknowledge those who share their data. The journal primarily publishes Data Descriptors, which offer detailed descriptions of research datasets, including data collection methods and technical analyses validating data quality. These descriptors aim to facilitate data reuse rather than testing hypotheses or presenting new interpretations, methods, or in-depth analyses.