Evidence map›Paper›PMID 41575626›Full record

ArticleGenes & genomics2026

High-quality chromosome-scale genome assembly and adaptive evolution analysis of Yangtze endemic Coreius guichenoti.

Jing Chen, Xianqi Peng, Lei Huang, Xialian Bu, Yu Zhao, Tao Qian, Jian Zhu, Huantao Qu, Jiayun Yao

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Article in Genes & genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed
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1 · What the graph read from it

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3 · Its place in the literature

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1 citing paper in PubMed.

  1. Should a Dorsal or Anal Scale Be Used for Microcharacteristics Analysis inAnimals : an open access journal from MDPI · 2026
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5 · Who and what money

Authors and funding

9 authors.

Jing ChenKey Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries (Zhejiang Freshwater Fishery Environmental Monitoring Station), Huzhou, 313001, China.ORCID 0000-0001-7395-716X
Xianqi PengKey Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries (Zhejiang Freshwater Fishery Environmental Monitoring Station), Huzhou, 313001, China.
Lei HuangKey Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries (Zhejiang Freshwater Fishery Environmental Monitoring Station), Huzhou, 313001, China.
Xialian BuKey Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries (Zhejiang Freshwater Fishery Environmental Monitoring Station), Huzhou, 313001, China.
Yu ZhaoHubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Hubei Yichang, 443100, China.
Tao QianKaihua County Aquatic Technology Promotion Station, Quzhou, China.
Jian ZhuHubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Hubei Yichang, 443100, China.
Huantao QuHubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Hubei Yichang, 443100, China. quhuantao35@163.com.
Jiayun YaoKey Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries (Zhejiang Freshwater Fishery Environmental Monitoring Station), Huzhou, 313001, China. yaojiayun@126.com.

Funding

Hubei Provincial Key Laboratory of Fish Resources Protection in the Three Gorges Project 2021045-ZHX
6 · The paper itself

Abstract

backgroundCoreius guichenoti is a critically endangered, nationally protected second-class endemic fish in the upper Yangtze River. Its wild population has declined sharply due to habitat degradation, overfishing, and dam construction, necessitating urgent conservation genomics resources.

objectiveTo generate a high-quality chromosome-level genome assembly for C. guichenoti to elucidate its adaptive evolution and support conservation strategies.

methodsWe integrated PacBio HiFi long-read sequencing and Hi-C scaffolding technologies for de novo genome assembly. Genome annotation included repeat masking, protein-coding gene prediction, and functional characterization using public databases. Comparative genomics and phylogenetic analyses were performed with 13 related fish species.

resultsA 1.10 Gb genome was assembled, with 93.56% of sequences anchored to 25 chromosomes (scaffold N50 = 41.37 Mb). Repeat elements constituted 58.26% of the genome, and 25,588 protein-coding genes were predicted (96.1% functionally annotated). BUSCO completeness reached 99.7%. Phylogenetic analysis revealed that C. guichenoti diverged from Leuciscus waleckii ~ 79.8 million years ago. Synteny analysis showed significant chromosomal rearrangements between these species. Gene family expansions implicated immune adaptation (e.g., IL-17 signaling) and metabolic pathways (e.g., arachidonic acid metabolism).

conclusionThis high-quality genome provides a critical resource for understanding adaptive evolution and guiding conservation strategies for this imperiled species.

Indexed as

CyprinidaeEvolution, MolecularGenomeAnimalsChromosomesGenomicsMolecular Sequence AnnotationPhylogenyChromosome-scale genome assemblyComparative genomicsCoreius guichenotiHi-C technologyPacBio HiFi reads

Identifiers

PMID41575626

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