Chromosome-Level Genome Assembly and Transcriptome Analysis of the
Chinese Bahaba (Bahaba taipingensis) Reveal Genomic Features and Tissue
Expression Patterns
Abstract
The Chinese bahaba (Bahaba taipingensis) is a critically endangered
species found in the coastal waters of the South China Sea, which has
garnered significant attention due to its ecological, economic, and
medicinal value. In this study, we present a high-quality genome
assembly of the Chinese bahaba. By employing a combination of Hifi,
Nanopore UL and Hi-C data, we assembled 686.86 Mb genome sequences,
consisting of 83 contigs with a contig N50 of 30.02 Mb. Then, the
initial assembly was further anchored onto 24 chromosomes, of which only
2 chromosomes have gaps. The enrichment analysis of expanded gene
families revealed the immune system characteristics in Sciaenidae fish
and Chinese bahaba. Notably, the fibrinogen complex of expanded gene
families in Chinese bahaba, along with multiple GO terms related to ion
binding, suggested potential roles in coagulation processes. An analysis
of selection pressure revealed 47 fast-evolving genes, including tcn2
and cd44, which may participate in hematopoiesis. The RNA-seq data from
9 tissues indicated the higher expression level of col1a1 and col1a2 in
swim bladder, which may contribute to the massive collagen deposition.
The assembled genome and transcriptome will provide insights into the
genetic basis of key biological traits, population genetics, and
evolutionary history.