Evidence map›Paper›PMID 40620001›Full record

ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2025

Subgenome Partitioning and Polyploid Genome Evolution in the Loach Family Botiidae (Order Cypriniformes).

Yunyun Lv, Jia Li, Yanping Li, Yu Huang, Qiang Lai, Zhengyong Wen, Jun Wang, Yang He, Jinrong Shi, Zejin Huang and 5 more

Abstract read
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In one paragraph

Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Yunyun LvKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.ORCID https://orcid.org/0009-0003-4941-268X
Jia LiLaboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518067, China.
Yanping LiKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.
Yu HuangState Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
Qiang LaiZizhong County Fishery Development Center, Neijiang, 641200, China.
Zhengyong WenKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.
Jun WangKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.
Yang HeKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.
Jinrong ShiKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.
Zejin HuangKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.
Ying JiangKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.
Yves Van de PeerDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium.
Qiong ShiKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.
Biwen XieKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.
Yongming WangKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang, 641100, China.

Funding

Ghent University BOF.MET.2021.0005.01National Natural Science Foundation of China 32200347Sichuan Provincial Science and Technology Support Program 2023NSFSC1238Sichuan Provincial Science and Technology Support Program 2025ZNSFSC1077
6 · The paper itself

Abstract

Vertebrates have undergone two rounds of whole-genome duplication (WGD), termed 1R and 2R, with a third, teleost-specific duplication (TSGD or 3R) occurring in ray-finned fishes. In the order Cypriniformes, additional lineage-specific WGDs have further contributed to species diversification. While polyploidy is well characterized in species like common carp and goldfish, other polyploid taxa-particularly loaches-remain understudied. Here, high-quality, chromosome-level genome assemblies are presented for two loach species: Sinibotia superciliaris (Golden Chinese Loach) and Parabotia fasciatus (Yichang Sand Loach). By integrating these genomes into a comparative framework with 20 other cypriniform species, key phylogenetic relationships are reconstructed, and introduce a novel subgenome partitioning method (M3). Unlike previous approaches, M3 uses differential sequence divergence to accurately and rapidly assign subgenomes, completing partitioning within minutes and outperforming existing tools. Applying M3, a markedly reduced subgenome is uncovered in the Golden Chinese Loach, with lineage-specific molecular changes in several candidate genes, suggesting potential adaptive significance. This study offers a comprehensive view of polyploidy and subgenome evolution in loaches, highlighting the genomic complexity shaped by repeated WGDs in Cypriniformes and providing valuable resources for future research on vertebrate genome evolution and adaptation.

Indexed as

CypriniformesEvolution, MolecularGenomePolyploidyAnimalsPhylogenyCypriniformesgenome evolutionloachespolyploidysubgenome partitioning

Identifiers

PMID40620001
PMCPMC12462953

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Registered trials

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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 OpenQuestion graph.