Whole-Genome Sequencing Reveals Autopolyploidy and Evolutionary Trajectory of Chinese Sturgeon

Background

Chinese sturgeon (Acipenser sinensis), as a member of the sturgeon subclass, is an ancient fish group. Due to its unique genome structure and economic value, the conservation and research of Chinese sturgeon are of great significance. Sturgeons are known as “living fossils” and have complex Whole-Genome Duplication (WGD) events. Understanding their ploidy evolution can provide important insights into fish evolution research. Previous studies have shown that polyploidy exists in sturgeons, including diploid, tetraploid, and octoploid forms. WGD is very common in fish evolution, and the genome of Chinese sturgeon is more challenging due to its complex polyploid characteristics. This study reveals the octoploid genome of Chinese sturgeon through whole-genome sequencing and explores its evolutionary path.

Research Source

This research was jointly completed by several scholars including Binzhong Wang, Bin Wu, Xueqing Liu, Yacheng Hu, and others. The authors are mainly from China Three Gorges Corporation, Key Laboratory of Yangtze River Fish Conservation, BGI-Shenzhen, Technical University of Denmark, and other institutions. This paper was published in the journal Genomics, Proteomics & Bioinformatics and was funded by China Three Gorges Corporation.

Research Process

Research Workflow

The study was divided into several main steps. First, researchers extracted DNA from Chinese sturgeon blood and performed whole-genome sequencing using Illumina platform, PacBio platform, and Hi-C technology. The sequencing yielded 421.58 GB of Illumina short-read data, 221.96 GB of PacBio long-read data, and 172.87 GB of Hi-C data. These data were then used for genome assembly and annotation.

Genome Assembly and Annotation

Researchers integrated de novo prediction, protein homology, and RNA sequencing data-assisted methods for gene structure prediction. A total of 36,837 protein-coding genes were predicted, with an average length of 14.3 kb, and the complete genome assembly includes 1.99 GB of chromosomes.

Synteny and Collinearity Analysis

To analyze the quality of genome assembly and chromosome evolution, researchers conducted collinearity analysis between Chinese sturgeon and other sturgeon species (such as sterlet and paddlefish) as well as related gar species (Lepisosteus oculatus). They also constructed an evolutionary tree through phylogenetic analysis.

Ploidy Characteristics and Genome Analysis

Traditional karyotype analysis showed that Chinese sturgeon has 264 chromosomes, four times that of common sturgeon (60 chromosomes), suggesting that Chinese sturgeon is octoploid. To further clarify the ploidy, researchers conducted whole-genome Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) analyses.

Research Results

High-Quality Genome Assembly

The study showed that the genome assembly quality of Chinese sturgeon is high, with clear pairwise collinearity between chromosomes. Mcscan analysis revealed a large number of clustered collinear genes in three sturgeon species. The constructed evolutionary tree showed that Chinese sturgeon and sterlet have a common sturgeon ancestor, while paddlefish is their sister lineage.

Octoploid Characteristics and Complex Ploidy Composition

Through detailed karyotype analysis and SNP depth sequencing, researchers found that Chinese sturgeon has octoploid characteristics. Smudgeplot analysis showed that the ploidy composition of Chinese sturgeon is extremely complex, including four types of octoploid k-mers, hexaploid, one tetraploid, and diploid, indicating that its genome has typical octoploid characteristics.

Autopolyploidy Revealed by Collinearity and TE Analysis

To analyze the ploidy composition of Chinese sturgeon, researchers used smudgeplot analysis to study representative tetraploid species’ allopolyploid and autopolyploid whole-genome duplication events. The results confirmed that Chinese sturgeon is an autopolyploid rather than an allopolyploid. Furthermore, through transposable element (TE) landscape analysis, no significant allopolyploid-specific transposon families were found in the Chinese sturgeon genome, further ruling out the possibility of allopolyploidy.

Whole-Genome Duplication and Species Origin Time Revealed by Ks Model

To more accurately infer WGD and divergence times, researchers used the Ks model combined with collinearity analysis to reveal the ploidy evolution of Chinese sturgeon. The results showed that Chinese sturgeon underwent two whole-genome duplication events, As3R 210.7 million years ago and Chinese sturgeon autotetraploidization (As4R) about 35.12 million years ago, and indicated that species divergence occurred 121.3 million years ago.

Research Conclusions

This study completed the first whole-genome sequencing of an octoploid fish, revealing the complex ploidy composition and evolutionary history of Chinese sturgeon. It provides valuable resources for gene conservation and evolutionary research of sturgeons and offers a reference for genome research of other polyploid vertebrates. WGD events are closely related to environmental changes in geological history, such as the impact of Earth impact events on the reproduction process of Chinese sturgeon ancestors.

Research Highlights

1. First Whole-Genome Sequencing: Chinese sturgeon is the first octoploid vertebrate to undergo whole-genome sequencing, showcasing complex genome composition and ploidy characteristics.
2. Providing Valuable Resources: High-quality genome resources will provide a powerful platform for genetic, evolutionary, and conservation research of sturgeons.
3. Refined WGD and Evolution Timing: The Ks model more accurately inferred whole-genome duplication and species origin times.

Significance and Value of the Research

This study provides deep insights into the evolution of polyploid fish and whole-genome duplication events, revealing the complex autopolyploid characteristics of Chinese sturgeon. It has important scientific and application value for the conservation, management, and future research of sturgeons. At the same time, it also provides an important genomic reference for genome research of other polyploid vertebrates.