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

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

doi:10.1038/s41597-025-04419-9

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

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

Authors

Ruoyu Liu¹, Ziyu Meng¹, Yinan Mu¹, Ran Zhang², Hanhui Ma¹, Jingjing Hu¹, Yanan Wang¹, Yuxin Shi¹, Yanan Li³, Chaofeng Wang¹, Weini Zhang¹, Longshan Lin⁴, Ping Zheng⁵, Xinhua Chen⁶

Affiliations

¹ 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.
² Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
³ Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510222, China.
⁴ Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China. linlongshan@tio.org.cn.
⁵ 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. zhengping13@mails.ucas.ac.cn.
⁶ 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. chenxinhua@tio.org.cn.

PMID: 39809797
DOI: 10.1038/s41597-025-04419-9

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.

Publication types

Dataset

MeSH terms

Animals
Arctic Regions
Chromosomes*
Fishes / genetics
Genome*
Molecular Sequence Annotation*

Abstract

Publication types

MeSH terms

Grants and funding