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<p>Deep-sea cold seeps form a benthic hypoxic biome characterized by low temperatures, methane venting, and metalliferous fluid emissions. This extreme environment was dominated by high-biomass species such as clams. While most studies have focused on the symbiotic function of cold seep clams, research on the roles of their non-symbiotic functions remains limited. In this study, we conducted transcriptome analysis to examine gene expression pattern in the testis, adductor muscle (hereinafter “muscle”), and foot of <i>Phreagena okutanii</i>, a clam species collected from the S11 site on the western slope of the Okinawa Trough. Principal component analysis and differential expression analysis revealed that the gene expression patterns of the muscle and foot tissues were shared more similar gene expression patterns with each other than with the testis. A total of 564 co-expressed genes with transcripts per million (TPM) &gt; 10 were identified as co-expressed genes in the testis, muscle, and foot. The gene expression patterns of hemoglobin I and II (<i>hb1, hb2</i>), heat shock proteins 70 and 90 (<i>hsp70, hsp90</i>), glutathione peroxidase (<i>GPx</i>), thioredoxin-2 (<i>Trx2</i>), and ferritin (<i>fer</i>) for oxygen transportation, stress response and antioxidation were identified in the three tissues. In particular, 4 853 and 6 194 differentially expressed genes (DEGs) were identified in the testis compared to the muscle and foot, respectively, significantly exceeding the 854 DEGs observed between the muscle and foot. Furthermore, DEG intersection enabled the identification of shared tissue-specific expression patterns, including genes that were upregulated in the testis relative to both the muscle and foot; those upregulated in the muscle relative to both the testis and foot, and those upregulated in the foot relative to both the testis and muscle. Antioxidant genes inhibited the production of reactive oxygen species and catalyzed their removal. The immune response gene played a key role in pathogen recognition and elimination. Energy metabolism genes enhanced energy production and accumulation, supporting adaptation to the high-sulfur and low-oxygen environments. Our study provides further insights into the gene expression pattern of bivalves in specialized deep-sea cold seep environments.</p>

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Transcriptome sequencing reveals gene expression patterns in non-symbiotic tissues of the cold seep clam Phreagena okutanii

  • 期刊论文

  • 发表日期：

    2025年10月1日

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  • Yinjun Ye,
  • Genmei Lin,
  • Huixin Zhao,
  • Xuanguang Liang,
  • Junrou Huang,
  • Jianguo Lu

摘要

Deep-sea cold seeps form a benthic hypoxic biome characterized by low temperatures, methane venting, and metalliferous fluid emissions. This extreme environment was dominated by high-biomass species such as clams. While most studies have focused on the symbiotic function of cold seep clams, research on the roles of their non-symbiotic functions remains limited. In this study, we conducted transcriptome analysis to examine gene expression pattern in the testis, adductor muscle (hereinafter “muscle”), and foot of Phreagena okutanii, a clam species collected from the S11 site on the western slope of the Okinawa Trough. Principal component analysis and differential expression analysis revealed that the gene expression patterns of the muscle and foot tissues were shared more similar gene expression patterns with each other than with the testis. A total of 564 co-expressed genes with transcripts per million (TPM) > 10 were identified as co-expressed genes in the testis, muscle, and foot. The gene expression patterns of hemoglobin I and II (hb1, hb2), heat shock proteins 70 and 90 (hsp70, hsp90), glutathione peroxidase (GPx), thioredoxin-2 (Trx2), and ferritin (fer) for oxygen transportation, stress response and antioxidation were identified in the three tissues. In particular, 4 853 and 6 194 differentially expressed genes (DEGs) were identified in the testis compared to the muscle and foot, respectively, significantly exceeding the 854 DEGs observed between the muscle and foot. Furthermore, DEG intersection enabled the identification of shared tissue-specific expression patterns, including genes that were upregulated in the testis relative to both the muscle and foot; those upregulated in the muscle relative to both the testis and foot, and those upregulated in the foot relative to both the testis and muscle. Antioxidant genes inhibited the production of reactive oxygen species and catalyzed their removal. The immune response gene played a key role in pathogen recognition and elimination. Energy metabolism genes enhanced energy production and accumulation, supporting adaptation to the high-sulfur and low-oxygen environments. Our study provides further insights into the gene expression pattern of bivalves in specialized deep-sea cold seep environments.