Evidence map›Paper›PMID 40598134›Full record

ArticleBMC biology2025

Construction of the graph genomes of Takifugu provides novel insights into the genomic mechanisms of population structure and migratory traits.

Rui-Shi He, Rong Zhao, Jun-Jie Lin, Yan Li, Xiang-Zhu Kong, Jin-Xuan Xu, Jing-Hang Wu, Xing-Jiang Bu, Yong-Jun Zhang, Yang Sun

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Article in BMC biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

10 authors.

Rui-Shi He *Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China.
Rong Zhao *Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China.
Jun-Jie LinKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China.
Yan LiKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China.
Xiang-Zhu KongKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China.
Jin-Xuan XuKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China.
Jing-Hang WuKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China.
Xing-Jiang BuKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China. buxingjiang@ahnu.edu.cn.
Yong-Jun ZhangKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China. yjzhang@ippcaas.cn.
Yang SunKey Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China. sy2019@ahnu.edu.cn.

Funding

Major Science and Technology Projects in Anhui Province 202003a06020009National Natural Science Foundation of China 31871964, 31801738, 32302320National Rice Industry Technology System Project CARS-01-40
6 · The paper itself

Abstract

backgroundThe genus Takifugu includes highly valued fish species known for their delicate flavor, making them popular in multiple countries. However, many species from this genus face significant threats. In order to better understand the genetic diversity and evolutionary dynamics of Takifugu, a syntelog-based pan-genome and graph genome were constructed using the data of seven Takifugu species.

resultsThe analysis of 28,085 syntelog groups (SGs) composed of protein-coding genes revealed that only 57.3% of the SGs were shared among all individuals, whereas the remaining genes presented presence-absence variation (PAV) across the seven genomes. Using the graph genome as a reference, a population of 160 Takifugu individuals was analyzed, from which 20,133,471 SNPs, 4,606,141 Indels, and 152,200 SVs were identified. The gene flow analysis revealed directional gene flow from Takifugu bimaculatus and Takifugu flavidus to Takifugu oblongus. Notably, a 51-bp insertion in the ABCB9 gene differed significantly in frequency between the two migratory populations, suggesting the potential role of this gene in the migratory behavior of these species. Additionally, the expression profiles from 13 tissues or organs (brain, gallbladder, gill, gonad, heart, kidney, liver, muscle, pituitary, skin, spleen, stomach, and swim bladder) revealed a unique expression pattern in the liver, with the tissue-specific genes exhibiting evolutionary conservation to varying degrees. The highest proportion of core genes was found in the pituitary, whereas the lowest was found in the spleen.

conclusionsThis study provides comprehensive genomic resources that enhance the understanding of the genetic diversity and evolutionary dynamics of Takifugu species. The findings offer insights for research on both breeding and conservation of Takifugu.

Indexed as

Animal MigrationGenetic VariationGenomeTakifuguAnimalsGene FlowGraph pan-genomePAVSVSynthetic-based pan-genomeTakifugu

Identifiers

PMID40598134
PMCPMC12220038

What Socratic holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.