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Biomolecules
Volume 15
Issue 12
10.3390/biom15121648
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Chromosome-Level Genome Assembly of Red Sea Bream (Pagrus major) Reveals Integration of Heterospecific Sperm-Derived Genetic Material in Artificial Gynogenesis

by
Mingyang Liu
1,2,3,
Guixing Wang
1,2,3,
Yuqin Ren
1,2,3,
Xiaoyan Zhang
1,2,3,
Bingbu Li
1,2,3,
Yitong Zhang
1,2,3,
Yucong Yang
1,2,3,
Lize San
1,2,3,* and
Jilun Hou
1,2,3,*
1
State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
2
Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
3
Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
*
Authors to whom correspondence should be addressed.
Biomolecules 2025, 15(12), 1648; https://doi.org/10.3390/biom15121648
Submission received: 23 September 2025 / Revised: 18 November 2025 / Accepted: 19 November 2025 / Published: 24 November 2025
(This article belongs to the Section Molecular Genetics)
Versions Notes

Abstract

Artificially induced gynogenesis, a technique that utilizes UV-irradiated sperm to activate eggs while excluding paternal genetic contribution, has been instrumental in the genetic improvement of aquaculture species. Although the allo-sperm effect has been observed in some freshwater fish and suggests the integration of paternal DNA, its occurrence and mechanisms in marine fish remain unclear. In this study, a 795.23 Mb chromosome-level genome assembly for red sea bream (Pagrus major) was presented, with a scaffold N50 of 32.03 Mb, encompassing 29,083 protein-coding genes. Furthermore, the allo-sperm effect was investigated on the artificial gynogenesis of Japanese flounder (Paralichthys olivaceus) induced by UV-irradiated P. major sperm. Whole-genome sequencing of gynogenetic and normal fertilized offspring revealed eight representative genomic sequences with >96.88% nucleotide identity to P. major, including six Sparidae-specific centromeric satellite DNA sequences. PCR validation and Sanger sequencing confirmed that these sequences were present exclusively in gynogenetic groups and absent in normally fertilized offspring, providing direct evidence of the allo-sperm effect. Our findings extend the allo-sperm effect to marine fish and demonstrate its potential across taxonomically distant taxa, P. olivaceus (Pleuronectiformes) × P. major (Spariformes). These results offer valuable genomic information for P. major, and provide important insights for future genetic breeding programs in aquaculture.
Keywords: Pagrus major; allo-sperm effect; genome; paternal-specific sequences; gene family expansion; centromeric satellite DNA; spermiogenesis Pagrus major; allo-sperm effect; genome; paternal-specific sequences; gene family expansion; centromeric satellite DNA; spermiogenesis

Share and Cite

MDPI and ACS Style

Liu, M.; Wang, G.; Ren, Y.; Zhang, X.; Li, B.; Zhang, Y.; Yang, Y.; San, L.; Hou, J. Chromosome-Level Genome Assembly of Red Sea Bream (Pagrus major) Reveals Integration of Heterospecific Sperm-Derived Genetic Material in Artificial Gynogenesis. Biomolecules 2025, 15, 1648. https://doi.org/10.3390/biom15121648

AMA Style

Liu M, Wang G, Ren Y, Zhang X, Li B, Zhang Y, Yang Y, San L, Hou J. Chromosome-Level Genome Assembly of Red Sea Bream (Pagrus major) Reveals Integration of Heterospecific Sperm-Derived Genetic Material in Artificial Gynogenesis. Biomolecules. 2025; 15(12):1648. https://doi.org/10.3390/biom15121648

Chicago/Turabian Style

Liu, Mingyang, Guixing Wang, Yuqin Ren, Xiaoyan Zhang, Bingbu Li, Yitong Zhang, Yucong Yang, Lize San, and Jilun Hou. 2025. "Chromosome-Level Genome Assembly of Red Sea Bream (Pagrus major) Reveals Integration of Heterospecific Sperm-Derived Genetic Material in Artificial Gynogenesis" Biomolecules 15, no. 12: 1648. https://doi.org/10.3390/biom15121648

APA Style

Liu, M., Wang, G., Ren, Y., Zhang, X., Li, B., Zhang, Y., Yang, Y., San, L., & Hou, J. (2025). Chromosome-Level Genome Assembly of Red Sea Bream (Pagrus major) Reveals Integration of Heterospecific Sperm-Derived Genetic Material in Artificial Gynogenesis. Biomolecules, 15(12), 1648. https://doi.org/10.3390/biom15121648

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