北极鱼类中脉拟狼鱼的染色体水平参考基因组及注释

Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius.

作者信息

Liu Ruoyu, Meng Ziyu, Mu Yinan, Zhang Ran, Ma Hanhui, Hu Jingjing, Wang Yanan, Shi Yuxin, Li Yanan, Wang Chaofeng, Zhang Weini, Lin Longshan, Zheng Ping, Chen Xinhua

机构信息

State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.

出版信息

Sci Data. 2025 Jan 14;12(1):68. doi: 10.1038/s41597-025-04419-9.

DOI:10.1038/s41597-025-04419-9

PMID:39809797

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11733169/

Abstract

Anisarchus medius (Reinhardt, 1837) is a widely distributed Arctic fish, serving as an indicator of climate change impacts on coastal Arctic ecosystems. This study presents a chromosome-level genome assembly for A. medius using PacBio sequencing and Hi-C technology. The PacBio assembly totaled 739.07 Mb across 697 contigs, with a Contig N50 of 10.004 Mb. Hi-C mapping yielded 23 chromosomes, with a successful mapping rate of 90.53% and a Scaffold N50 of 30.20 Mb. Genome BUSCO integrity was 97.05%. Repetitive sequences accounted for 240.83 Mb (32.58%) of the genome. Non-coding RNA annotations included 4,928 rRNAs, 9,663 tRNAs, 347 snRNAs, and 21 snoRNAs. A total of 30,345 protein-coding genes were identified, encoding 46,603 proteins, with a BUSCO completeness of 94.98%. Molecular pathway related to the endocrine system, carbohydrate metabolism, folding, sorting, and degradation, signal transduction, and transport and catabolism contribute to A. medius adaptation to extreme Arctic environments. This high-quality genome provides valuable genetic resources for understanding Arctic adaptations and supporting polar ecological conservation and management.

摘要

中拟三刺鲀（Reinhardt，1837年）是一种广泛分布于北极地区的鱼类，可作为气候变化对北极沿海生态系统影响的指示物种。本研究利用PacBio测序和Hi-C技术，对中拟三刺鲀进行了染色体水平的基因组组装。PacBio组装结果共得到739.07 Mb，分布在697个重叠群中，重叠群N50为10.004 Mb。Hi-C图谱构建得到23条染色体，成功映射率为90.53%，支架N50为30.20 Mb。基因组BUSCO完整性为97.05%。重复序列占基因组的240.83 Mb（32.58%）。非编码RNA注释包括4928个rRNA、9663个tRNA、347个snRNA和21个snoRNA。共鉴定出30345个蛋白质编码基因，编码46603种蛋白质，BUSCO完整性为94.98%。与内分泌系统、碳水化合物代谢、折叠、分选和降解、信号转导以及运输和分解代谢相关的分子途径有助于中拟三刺鲀适应极端的北极环境。这种高质量的基因组为理解北极适应性以及支持极地生态保护和管理提供了宝贵的遗传资源。