A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape

The remarkable morphological diversity and species abundance of teleost fishes offer a valuable resource for understanding vertebrate evolution. In phase I of the Fish10K project, genomes of 110 teleost species were sequenced and assembled, filling gaps in 3 previously unrepresented orders, and integrated with existing data to generate a 464 species whole-genome alignment spanning all teleost orders-the largest such resource beyond mammals and birds. Comparative analyses reveal distinctive genomic features, including progressive genome compaction with shortened intron lengths relative to non-teleost ray-finned fishes. Analysis of the transposable element (TE) landscape suggests a potential association between TE expansion in teleost genomes and different habitats, as well as the uniqueness of teleosts' DNA-dominated transposon composition among vertebrates. Genome-wide phylogenetic analyses refute the widely accepted monophyly of "Siluriphysi" hypothesis and support the hypothesis of a single origin of electroreception followed by secondary loss in Characiformes. A refined evolutionary timeline of teleosts by whole-genome alignment resource placed teleosts at ∼253 million years ago, predating the Permian-Triassic extinction, and delineates three diversification phases punctuated by mass extinctions, challenging continuous post-Cretaceous-Palaeogene acceleration models. This study establishes a large-scale genomic database and a foundational whole-genome alignment resource, advancing insights into the landscape of teleost genomic architecture and macroevolution.

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Publication Details

Journal
The Innovation
Published
2025-11-06
DOI
https://doi.org/10.1016/j.xinn.2025.101177
Primary Topic
Ichthyology and Marine Biology
Type
article
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article

A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape

Yuanning Li, He Zhang, Huanming Yang, Song He et al.
The Innovation
Ichthyology and Marine Biology
article

A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape

Yuanning Li, He Zhang, Huanming Yang, Song He, Liandong Yang, Inge Seim, Suyu Zhang, Karsten Kristiansen, Zhaohui Pan, Jian‐Fang Gui, Xiao Chen, Jian Liang, Mengjun Wang, You-an Zhu, Honghui Zeng, Hongyue Liu, Meiru Liu, Qingming Qu, Shanshan Liu, Simon Ming‐Yuen Lee, Guangyi Fan, Guojie Zhang, Xun Xu, Qiang Qiu, Zengbao Yuan, Yue Song, Xiaolin Tian, Mengjun Yu, Hanbo Li, Mingliang Hu, Yaolei Zhang, Jiahao Wang, Xin Liu, Kun Wang, Jian Wang, Wen Wang, Yongxin Li, Yonghua Sun, Cheng Wang, Qun Liu, Chenglong Liu, Mengqi Zhang, Xiaoni Gan, Gang Hou, Feng Chen, Shunping He, Yi‐Yu Chen, Chenglong Zhu, Hengjia Yang, Chengchi Fang, Wenjie Xu, Zhuocheng Zhou, Luyuan Pan
article en

Abstract

The remarkable morphological diversity and species abundance of teleost fishes offer a valuable resource for understanding vertebrate evolution. In phase I of the Fish10K project, genomes of 110 teleost species were sequenced and assembled, filling gaps in 3 previously unrepresented orders, and integrated with existing data to generate a 464 species whole-genome alignment spanning all teleost orders-the largest such resource beyond mammals and birds. Comparative analyses reveal distinctive genomic features, including progressive genome compaction with shortened intron lengths relative to non-teleost ray-finned fishes. Analysis of the transposable element (TE) landscape suggests a potential association between TE expansion in teleost genomes and different habitats, as well as the uniqueness of teleosts' DNA-dominated transposon composition among vertebrates. Genome-wide phylogenetic analyses refute the widely accepted monophyly of "Siluriphysi" hypothesis and support the hypothesis of a single origin of electroreception followed by secondary loss in Characiformes. A refined evolutionary timeline of teleosts by whole-genome alignment resource placed teleosts at ∼253 million years ago, predating the Permian-Triassic extinction, and delineates three diversification phases punctuated by mass extinctions, challenging continuous post-Cretaceous-Palaeogene acceleration models. This study establishes a large-scale genomic database and a foundational whole-genome alignment resource, advancing insights into the landscape of teleost genomic architecture and macroevolution.

The InnovationVol. 7(3)
BGI Group (China) (CN), South China Agricultural University (CN), Qinghai University (CN), University of Copenhagen (DK), Southwest University (CN), Hong Kong Polytechnic University (HK), Northwestern Polytechnical University (CN), Kunming Institute of Zoology (CN), Xiamen University (CN), Chinese Academy of Sciences (CN), Institute of Vertebrate Paleontology and Paleoanthropology (CN), Institute of Hydrobiology (CN), Women's Hospital, School of Medicine, Zhejiang University (CN), Cancer Hospital of Chinese Academy of Medical Sciences (CN), Institute of Deep-Sea Science and Engineering (CN), University of Chinese Academy of Sciences (CN), BGI Research (CN), Chinese Academy of Fishery Sciences (CN), King Abdullah University of Science and Technology (SA), Zhejiang University (CN), Guangdong Ocean University (CN), Shandong University of Science and Technology (CN), IT University of Copenhagen (DK)
Openalex Percentile: Top 68%
Ichthyology and Marine Biology
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