The global oyster industry, a powerhouse generating approximately 7 million metric tons annually, is in a constant pursuit of genetic innovation to meet worldwide demand. In this context, an international team of researchers has marked a watershed moment: the publication of the first chromosome-level genome assembly of an allotetraploid oyster.
The study, recently published in Scientific Data, details the genetic map of a hybrid between the Pacific oyster (Crassostrea gigas) and the Portuguese oyster (Crassostrea angulata). This resource promises to be the cornerstone for understanding the biology of duplicated genomes and optimizing polyploid breeding in modern aquaculture.
Key findings
- Global premiere: The first chromosome-level genome assembly of an allotetraploid oyster (C. gigas × C. angulata).
- Massive data: The assembled genome spans 1.23 Gb and contains 58,330 protein-coding genes.
- Stability: Allotetraploids may offer greater genomic stability for seed production compared to autotetraploids.
- Genetic interaction: The study confirms the presence and cooperation of subgenomes from both parental species.
The importance of tetraploids in the industry
To understand the magnitude of this breakthrough, we must look at commercial production. Triploid oysters (3n) are the driving force of modern aquaculture, accounting for 30% to 70% of production in leading markets such as France, the United States, and China.
These oysters are highly valued for three competitive factors:
- Accelerated Growth: Faster time-to-market size due to heterozygosity.
- Sterility: By not expending energy on reproduction, they maintain superior meat quality year-round.
- Environmental Safety: Their sterility minimizes the risk of genetic impact on wild populations.
To produce these triploid oysters commercially and safely (without chemical induction), diploid oysters (2n) are crossed with tetraploids (4n). Until now, most tetraploids were single-species (autotetraploids). However, allotetraploids (hybrids of two species) could offer superior advantages by combining desirable traits from both parents and providing greater genomic stability.
A deep dive into the hybrid genome
Using cutting-edge sequencing technologies (PacBio, Illumina, and Hi-C), scientists assembled a high-fidelity genome that reveals the organism’s complexity:
- Genome Size: 1.23 Gb.
- Organization: 90% of sequences were successfully anchored to 20 chromosomes.
- Functional Richness: 58,330 protein-coding genes were predicted, with an impressive 98.34% functionally annotated.
- Composition: Approximately 46.43% of the genome consists of repetitive sequences.
This level of precision allows for the observation of the “reorganization” that occurs when two distinct genomes unite and duplicate, offering a unique window into the evolution of polyploids.
Confirmation of the hybrid nature
The team not only sequenced but also technically validated that the oyster was a true allotetraploid hybrid. Through collinearity analysis, they confirmed highly conserved gene blocks between the hybrid and the parental species. Furthermore, mitochondrial analysis verified that the mitochondrial genome originated from C. angulata, matching the pedigree of the laboratory cross and confirming biparental inheritance.
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Implications for the future of aquaculture
The availability of this genome heralds a new era for genetic improvement in mollusks.
“Having this complete genomic sequence gives oyster breeders a powerful new resource. By understanding how the genes from these two species work together in a hybrid, we can potentially develop more resilient oyster stocks and make the aquaculture industry more efficient and sustainable.” — Dr. Ximing Guo, co-author of the study.
In practice, this knowledge will allow researchers to:
- Study genomic interaction: Analyze how genes from distinct species cooperate or compete.
- Develop new varieties: Create combinations that improve disease resistance and growth rates.
- Stabilize production: Facilitate the use of stable allotetraploid broodstock for mass seed production.
This scientific advancement is not merely an academic achievement; it is a practical tool designed to bolster the sustainability and profitability of oyster farming globally.
Reference (open access)
Li, A., Zhao, M., Zhao, J., Zhang, M., Huo, M., Deng, J., Wang, L., Wang, W., Qi, H., Li, Y., Li, X., Fu, J., Guo, X., Xu, Z., Li, L., Guo, X., & Zhang, G. (2025). Chromosomal-level genome assembly of an allotetraploid oyster. Scientific Data, 12(1), 1492. https://doi.org/10.1038/s41597-025-05775-2
Editor at the digital magazine AquaHoy. He holds a degree in Aquaculture Biology from the National University of Santa (UNS) and a Master’s degree in Science and Innovation Management from the Polytechnic University of Valencia, with postgraduate diplomas in Business Innovation and Innovation Management. He possesses extensive experience in the aquaculture and fisheries sector, having led the Fisheries Innovation Unit of the National Program for Innovation in Fisheries and Aquaculture (PNIPA). He has served as a senior consultant in technology watch, an innovation project formulator and advisor, and a lecturer at UNS. He is a member of the Peruvian College of Biologists and was recognized by the World Aquaculture Society (WAS) in 2016 for his contribution to aquaculture.
