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Chromosome-Level Genome Assembly and Transcriptome Analysis of the Chinese Bahaba (Bahaba taipingensis) Reveal Genomic Features and Tissue Expression Patterns
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  • Ming Li,
  • ma zehao,
  • gong zhihong,
  • Wenteng Xu,
  • Zhangfan Chen,
  • Luo Xinhui,
  • Yan Kuoqiu ,
  • Songlin Chen
Ming Li
Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute
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gong zhihong
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Wenteng Xu
Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
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Zhangfan Chen
Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
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Luo Xinhui
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Yan Kuoqiu
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Songlin Chen
Yellow Sea Fisheries Research Institute

Corresponding Author:[email protected]

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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.