Abstract:
【Objective】 This study aimed to investigate the phylogenetic relationships and whole-genome duplication (WGD) events across seven sturgeon species, and clarify the characteristics of highly replicated genes in octoploid sturgeons and expansion time of hemoglobin gene family, providing a theoretical basis for revealing genome duplication events and evolutionary strategies of Acipenseriformes.【Method】 Blood samples were collected from three tetraploid sturgeon species (
Acipenser stellatus,
Acipenser ruthenus, and
Huso huso) and four octoploid species (
Acipenser gueldenstaedtii,
Acipenser schrenckii,
Huso dauricus, and
Acipenser sinensis). Draft genomes were constructed using Illumina sequencing data. Gene family expansion and contraction events were analyzed through gene family analysis and phylogenetic tree reconstruction. WGD event timing was estimated based on synonymous substitution rates (
Ks) and fourfold degenerate site synonymous codon transversion rates (4DTv). Evolutionary analysis of the hemoglobin gene family was used to infer divergence times. Highly replicated genes that were amplified and retained during octoploidization were screened by comparing genomic coverage depths between octoploid and tetraploid sturgeons. These genes were further analyzed using KEGG signaling pathway enrichment and protein-protein interaction (PPI) networks.【Result】 The seven sturgeon genomes contained a large number of multi-copy orthologs, whereas the number of shared single-copy orthologs was extremely low (only 26). Obvious expansion and contraction events of gene families were observed among sturgeons of different ploidies, with distinct gene retention patterns between tetraploid and octoploid species. Comprehensive analysis of 4DTv and
Ks results showed that all sturgeons experienced an ancient Acipenseriformes-specific WGD event (As3R), approximately 118-196 million years ago, coinciding roughly with the period of the Permian-Triassic extinction event. Octoploid sturgeons showed significant differentiation in hemoglobin gene copy numbers: the ratio of α-hemoglobin gene copies was
Huso dauricus∶
Acipenser gueldenstaedtii∶
Acipenser schrenckii∶
Acipenser sinensis=3∶5∶4∶8, while the ratio for β-hemoglobin was
Huso dauricus∶
Acipenser gueldenstaedtii∶
Acipenser schrenckii∶
Acipenser sinensis=4∶20∶4∶8. A total of 219 highly replicated genes significantly that expanded and retained in octoploid sturgeons were primarily enriched in pathways related to basal metabolic processes, genomic stability, and expression regulation. The diagram of PPI networks revealed that core genes (
PPFIA2,
ZAP70, and
IRG1) played key roles in nervous system development and immune regulation.【Conclusion】 WGD events result in the high replication of genes in signaling pathways such as spliceosomal complex and DNA repair in octoploid sturgeons. This enhances the regulation of genomic stability and RNA processing, helping to avoid instability caused by increased redundant DNA. Consequently, octoploid sturgeon possesses more obvious advantages in physiological regulation, gene stability, and environmental adaptability.