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<p>The Chinese bahaba (<i>Bahaba taipingensis</i>) is a critically endangered species found in the coastal waters of the South China Sea and East 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 PacBio HiFi, ONT ultra-long and Hi-C sequencing 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 contain 3 gaps and 8 have telomeres at both ends. Percentages of 96.5% of complete BUSCOs were achieved, and a total of 22,100 protein-coding genes were annotated. We performed transcriptome analysis across nine tissues (heart, intestine, kidney, liver, muscle, skin, spleen, stomach, swim bladder). The result revealed higher expression levels of <i>col1a1</i> and <i>col1a2</i> in swim bladder, which may contribute to massive collagen deposition in this tissue. This high-quality assembly provides a valuable resource for studying the genetic basis of key biological traits (e.g., swim bladder collagen synthesis, otolith development) and will assist future investigations into the conservation genomics of <i>B. taipingensis</i>.</p>

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Chromosome-Level Genome Assembly and Transcriptome Analysis of the Chinese Bahaba (Bahaba taipingensis)

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年6月29日

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  • Ming Li,
  • Wenteng Xu,
  • Zehao Ma,
  • Zhihong Gong,
  • Zhangfan Chen,
  • Xinhui Luo,
  • Xihong Li,
  • Yu Zhai,
  • Kuoqiu Yan,
  • Songlin Chen

摘要

The Chinese bahaba (Bahaba taipingensis) is a critically endangered species found in the coastal waters of the South China Sea and East 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 PacBio HiFi, ONT ultra-long and Hi-C sequencing 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 contain 3 gaps and 8 have telomeres at both ends. Percentages of 96.5% of complete BUSCOs were achieved, and a total of 22,100 protein-coding genes were annotated. We performed transcriptome analysis across nine tissues (heart, intestine, kidney, liver, muscle, skin, spleen, stomach, swim bladder). The result revealed higher expression levels of col1a1 and col1a2 in swim bladder, which may contribute to massive collagen deposition in this tissue. This high-quality assembly provides a valuable resource for studying the genetic basis of key biological traits (e.g., swim bladder collagen synthesis, otolith development) and will assist future investigations into the conservation genomics of B. taipingensis.