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<p><i>Sicyopus rubicundus</i> belongs to the subfamily Sicydiinae in one of the largest fish families (Gobiidae) and has high ornamental value. However, its origin, evolution, and phylogenetic status remain unknown. Therefore, we aimed to better understand these aspects of this species. High-throughput sequencing was used to obtain its mitochondrial genome sequence, which had a total length of 16,499&#xa0;bp, and a structural analysis of the entire sequence was conducted. The base content of the mitochondrial genome exhibited a AT preference and included 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Except for <i>nad6</i> in the negative chain, all protein-coding genes were in the positive chain. The mitochondrial genome exhibited gene overlap and a tight arrangement, with overlapping sequences ranging from 1 to 7&#xa0;bp, a total length of 21&#xa0;bp, and six total locations, and gene spacer sequences ranging from 1 to 34&#xa0;bp, with a total length of 58&#xa0;bp and 11 total locations. Using maximum likelihood and Bayesian methods, a phylogenetic tree was constructed based on 29 mitochondrial whole-genome sequences of Sicydiinae species, and <i>S. rubicundus</i> had the closest genetic relationship with <i>Sicyopus zosterophorus</i>. This study provides a foundation for the protection of this species.</p>

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Phylogenetic position of Sicyopus rubicundus supported by annotated sequence of complete mitochondrial genome

  • 期刊论文

  • 发表日期：

    2025年2月20日

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  • Cheng-He Sun,
  • Xiao-Die Chen,
  • Jian-Qi Liu,
  • Chang-Hu Lu

摘要

Sicyopus rubicundus belongs to the subfamily Sicydiinae in one of the largest fish families (Gobiidae) and has high ornamental value. However, its origin, evolution, and phylogenetic status remain unknown. Therefore, we aimed to better understand these aspects of this species. High-throughput sequencing was used to obtain its mitochondrial genome sequence, which had a total length of 16,499 bp, and a structural analysis of the entire sequence was conducted. The base content of the mitochondrial genome exhibited a AT preference and included 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Except for nad6 in the negative chain, all protein-coding genes were in the positive chain. The mitochondrial genome exhibited gene overlap and a tight arrangement, with overlapping sequences ranging from 1 to 7 bp, a total length of 21 bp, and six total locations, and gene spacer sequences ranging from 1 to 34 bp, with a total length of 58 bp and 11 total locations. Using maximum likelihood and Bayesian methods, a phylogenetic tree was constructed based on 29 mitochondrial whole-genome sequences of Sicydiinae species, and S. rubicundus had the closest genetic relationship with Sicyopus zosterophorus. This study provides a foundation for the protection of this species.