Discussion
The Chinese bahaba’s swim bladder has been highlighted by U.S. media as one of the ”world’s nine most expensive foods” due to its unique properties and high medicinal value. Often referred to as ”the king of fish glue” and described as ”as valuable as gold,” the swim bladder’s rarity is largely attributed to its ability to prevent maternal hemorrhage. Its value and rarity have greatly attracted the interest of researchers and the market. High-quality reference genome sequences and transcriptome data provide a crucial foundation for further study.
The gene family expansion analysis in Chinese bahaba provides significant insights into the biological underpinnings of its medicinal properties. The expanded gene families enriched in various KEGG pathways and GO terms highlight a range of biological processes that could explain the its efficacy in general health benefits and hemostasis. One of the most notable findings from the enrichment analysis is the emphasis on immune-related functions. The expansion of gene families involved in immune response, complement activation, and pattern recognition receptors suggests that the Chinese bahaba has evolved robust defense mechanisms against pathogens. This immune fortification could be critical in helping the fish protect itself from infections and other environmental challenges. Another key aspect of the expanded gene families is their involvement in cell adhesion and tissue repair processes, as evidenced by the significant enrichment in pathways related to cell adhesion molecules, cytoskeletal components, and glycosaminoglycan biosynthesis, proteoglycans, other glycan degradation and glycosyltransferases. These genes likely contribute to the structural stability and resilience, which is essential for its overall health. It is reported that fish maw contains a high level of glycosaminoglycans, which have the effects of anti-tumor, anti-cancer, anti-virus, anti-thrombosis, and immune regulation (Pan et al., 2018; Ticar et al., 2020). Furthermore, the enrichment of genes related to oxidoreductase activity and cytochrome P450 enzymes indicates a strong antioxidant defense system. These enzymes play a crucial role in protecting tissues from oxidative damage. Additionally, the enrichment of genes associated with heme binding and iron metabolism suggests that Chinese bahaba has evolved mechanisms to regulate iron storage and utilization effectively. Ingesting fish maw could help supplement iron levels in the human body, which is particularly beneficial in treating anemia and improving blood production, further supporting recovery in postpartum women.
Further, we identified gene expansion for the fibrinogen alpha chain of GO term platelet activation in the Chinese bahaba than in other reference fishes. This gene encodes the alpha subunit of the coagulation factor fibrinogen, which is a component of the blood clot. Following vascular injury, the encoded preproprotein is proteolytically processed by thrombin during the conversion of fibrinogen to fibrin. The positive selection analysis also provided us with some hints. The transcobalamin-2 (tcn2 ) gene, also known as transcobalamin II or vitamin B12-binding protein 2, is a plasma protein. It is primarily involved in the transport and metabolism of vitamin B12 (cobalamin), a process that is crucial for blood cell regeneration, particularly red blood cell production. The cd44 gene is related to the hematopoietic cell lineage. The protein encoded by this gene is a cell-surface glycoprotein involved in cell-cell interactions, cell adhesion and migration. It is a receptor for hyaluronic acid and can also interact with other ligands, such as osteopontin, collagens, and matrix metalloproteinases. This protein participates in a wide variety of cellular functions including lymphocyte activation, recirculation and homing, and hematopoiesis. The link between these expanded or positively selected gene families and the prevention of haemorrhage in the swim bladder of the Chinese bahaba remains to be explored.
Fish maw collagen has excellent biocompatibility, low immunogenicity, degradability, and high direct cell adhesion ability. It has significant effects in enhancing immunity, activating tissue cells, inhibiting cancer cells, antioxidation, and hemostasis. In this study, the transcriptome data showed that the gene col1a1 and col1a2 were highly expressed in swim bladder of Chinese bahaba. Compared with other tissues, col6a6 and col10a1 were also mainly expressed in fish swim bladder. As most of the collagen genes were lowly expressed, it was inferred that the higher expression level ofcol1a1 and col1a2 could contribute to the massive collagen deposition in swim bladder.
To explore the molecular basis behind the unique morphological features of otolith in the Sciaenidae fishes, we conducted evolutionary analyses for otolith growth-related genes. It was found that the sparcl1 gene of Chinese bahaba was most likely to have been under positive selection. This is consistent with the study of C. lucidus , in which sparcl1 has been suggested to be closely associated with otolith growth [9]. There are three conserved structural domains within Sparc1, which are acidic calcium-binding domain I, follistatin-like domain II, and extra cellular calcium-binding domain III (Kawasaki, Suzuki, & Weiss, 2004). We found that most of the three structural domains of Sparcl1 were conserved, but there were some sites that differed from all other fish. For example, amino acid 511 is alanine (A) in all other fish, but serine (S) in both Chinese bahaba and large yellow croaker. Similarly, amino acid 613 is S in other fish, but A in the Chinese bahaba and large yellow croaker. Mutations in these amino acid sites may cause large structural and functional effects on proteins, which may affect the otolith formation in the Sciaenidae fishes.
In conclusion, we assembled a high quality genome of the Chinese bahaba, of which 8 chromosomes have telomeres at both ends, and only 2 chromosomes have gaps. Further genomic analysis revealed expanded gene families related to the immune systems and platelet activation, and fast-evolving genes being involved in hematopoiesis. The RNA-seq data from 9 tissues indicated that col1a1 and col1a2 expressed in swim bladder may contribute to the massive collagen deposition. Our resources will lay the foundation for the further genetic studies and accelerate the genetic breeding process of Chinese bahaba.