A chromosome-level genome assembly of the Chinese herring (Ilisha elongata) uncovered its population dynamics and genes related to lipid metabolism
文献类型： 外文期刊
作者： Wu, Tianqin 1 ; Hu, Jiantao 1 ; Giap, Vanthu 1 ; Wang, Qian 3 ; Lu, Liang 1 ; Li, Chenhong 1 ;
作者机构： 1.Shanghai Ocean Univ, Shanghai Univ Key Lab Marine Anim Taxon & Evolut, Shanghai, Peoples R China
2.Shanghai Ocean Univ, Engn Res Ctr Environm DNA & Ecol Water Hlth Assess, Shanghai, Peoples R China
3.Chinese Acad Fishery Sci, East China Sea Fisheries Res Inst, Shanghai, Peoples R China
关键词： chromosomal assembly; Ilisha elongata; fatty acid; genome annotation; population structure; the Northwest Pacific
期刊名称：JOURNAL OF HEREDITY （ 影响因子：2.5； 五年影响因子：2.6 ）
ISSN： 0022-1503
年卷期： 2025 年
页码：
收录情况： SCI
摘要： The Chinese herring (Ilisha elongata) is an economically important clupeiform fish, mostly found along the coast of China and Japan in the western Pacific Ocean. Overfishing and climate change have caused a substantial decline in its annual catch, which may have impacted its population size and structure. Here, we present a chromosome-level genome assembly of the Chinese herring, generated using a combination of Nanopore sequencing, Illumina sequencing, and high-throughput chromatin conformation capture technologies. The total length of this assembly is 802.47 Mbp, anchored to 24 chromosomes, with contig N50 and scaffold N50 values of 13.22 and 33.10 Mbp, respectively. Benchmarking Universal Single-Copy Orthologues analysis indicated high completeness of this assembly, with 94.9% of universal single-copy orthologs. Analysis of resequencing samples from various coastal regions of China and Japan revealed four distinct genetic populations of Chinese herring along the East Asian coast. The Dandong population (Yellow Sea) diverged earliest, exhibiting unique genetic structures and selective sweep signals, whereas the other three populations expanded from a tropical South China Sea ancestral population to the East China Sea and to Japanese waters. Among 23,366 protein-coding genes, several families related to the metabolism of very-long-chain unsaturated fatty acids are particularly contracted compared with the American shad. Additionally, several genes associated with fatty acid synthesis formation have undergone accelerated positive selection. These findings may explain the differential fatty acid ratios in marine versus riverine migratory clupeiforms. This high-quality genome assembly of the Chinese herring may provide valuable resources for comparative study of coastal fishes and benefit the development of a sustainable management strategy for fisheries of the Chinese herring.
- 相关文献
作者其他论文 更多>>
-
Flow Velocity Modulates Growth, Oxidative Stress, and Transcriptomic Responses in Spotted Sea Bass (Lateolabrax maculatus)
作者：Li, Shuo;Wang, Qian;Liu, Baoliang;Shao, Changwei;Li, Shuo;Liu, Yuyan;Wang, Qian;Zhu, Zhiwen;Li, Weijing;Li, Chen;Fei, Fan;Liu, Baoliang;Shao, Changwei;Liu, Yuyan;Wang, Qian;Shao, Changwei
关键词：Spotted sea bass; Flow velocity; Oxidative stress; Lipid metabolism; Transcriptomics
-
Near complete genome assembly of Yadong trout (Salmo trutta)
作者：Li, Chen;Han, Shenglei;Li, Shuo;Liu, Kaiqiang;Liu, Yuyan;Wang, Hong-yan;Wang, Qian;Liu, Changlin;Shao, Changwei;Li, Chen;Li, Chen;Han, Shenglei;Li, Shuo;Liu, Kaiqiang;Liu, Yuyan;Wang, Hong-yan;Wang, Qian;Liu, Changlin;Shao, Changwei;Liu, Kaiqiang;Liu, Yuyan;Wang, Hong-yan;Wang, Qian;Shao, Changwei
关键词：
-
Establishment and identification of spleen cell line from tiger puffer fish (Takifugu rubripes) and immune transcriptome response to IHNV
作者：He, Yangbin;Zhang, Jingjing;Meng, Bo;He, Yangbin;Zhang, Jingjing;Lin, Lei;Meng, Bo;Dong, Caichao;Liu, Yuyan;Yang, Yu;Ji, Honglong;Liu, Kaiqiang;Wang, Qian;Shao, Changwei;Liu, Yuyan;Liu, Kaiqiang;Wang, Qian;Shao, Changwei;Liu, Yuyan;Liu, Kaiqiang;Wang, Qian;Shao, Changwei
关键词：Tiger puffer fish; Spleen; Cell line; Immunology; Transcriptome
-
High-quality chromosome-level genome assembly of the whitespotted conger (Conger myriaster)
作者：Han, Shenglei;Han, Shenglei;Li, Chen;Li, Shuo;Chen, Yan;Liu, Kaiqiang;Liu, Yuyan;Wang, Hong-Yan;Wang, Qian;Cao, Xuwen;Shi, Bao;Shao, Changwei;Han, Shenglei;Li, Chen;Li, Shuo;Chen, Yan;Liu, Kaiqiang;Liu, Yuyan;Wang, Hong-Yan;Wang, Qian;Cao, Xuwen;Shi, Bao;Shao, Changwei;Wang, Chenggang;Liu, Kaiqiang;Liu, Yuyan;Wang, Hong-Yan;Wang, Qian;Cao, Xuwen;Shao, Changwei
关键词：
-
Population Patterns and Dynamics of Ilisha elongata (Clupeiformes: Pristigasteridae) Revealed by Target Enrichment Data
作者：Wang, Qian;Wang, Qian;Hu, Jiantao;Wu, Tianqin;Li, Chenhong;Hu, Jiantao;Wu, Tianqin;Li, Chenhong;Wang, Wenhao;Zhang, Jie;Kim, Jin-Koo
关键词：fisheries management;
Ilisha elongata -
The Primary Cultivation of Oogonial Stem Cells from Black Rockfish (Sebastes schlegelii): Morphology and Transcriptome Landscape
作者：Zhang, Jingjing;Lin, Lei;Zhu, Shengyu;Zhang, Yanming;Dong, Caichao;Yang, Yu;Liu, Yuyan;Cao, Xuwen;He, Yangbin;Ji, Honglong;Meng, Bo;Wang, Qian;Shao, Changwei;Zhang, Jingjing;Lin, Lei;Zhu, Shengyu;Zhang, Yanming;Dong, Caichao;Yang, Yu;Liu, Yuyan;Cao, Xuwen;He, Yangbin;Ji, Honglong;Meng, Bo;Wang, Qian;Shao, Changwei;Zhang, Jingjing;Zhu, Shengyu;Zhang, Yanming;He, Yangbin;Meng, Bo;Liu, Yuyan;Cao, Xuwen;Wang, Qian;Shao, Changwei
关键词：
Sebastes schlegelii ; oogonial stem cell; primary cultivation; cell metabolism; cell cycle -
Functional stomach loss preceding body inflation evolution in Tetraodontiformes: Evidence of gene loss and rapid evolution
作者：Liu, Chang;Lin, Lei;Du, Sheng;Liu, Kaiqiang;Ji, Honglong;Wang, Qian;He, Yangbin;Shao, Changwei;Liu, Kaiqiang;Wang, Qian;Shao, Changwei
关键词：Tetraodontiformes; Acid-peptic digestion; Convergent evolution; Gene loss; Rapid evolution
