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.