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<p><i>Cyclocarya paliurus</i>, a rare Chinese endemic known as the “sweet tea tree,” possesses significant hypoglycemic properties and holds dual status as both a traditional health beverage and an approved novel food ingredient. Despite extensive phytochemical research, its complete mitochondrial genome remained uncharacterized. This study reports the first assembly and annotation of the <i>Cyclocarya paliurus</i> mitogenome using PacBio HiFi long-read sequencing. The mitochondrial genome consists of two circular molecules (398,659&#xa0;bp and 355,751&#xa0;bp), featuring a stable GC content (~ 45%) and ranking among the largest within the Juglandaceae. Genome annotation revealed 75 functional genes, including 45 PCGs, 26 tRNAs, and 3 rRNAs. With the elevated tRNA count suggesting specialized roles in translational regulation. Predicted RNA editing identified 616 sites, predominantly causing hydrophilic-to-hydrophobic substitutions, while codon usage analysis confirmed a strong A/T-end bias. Repetitive sequence analysis uncovered abundant SSRs and dispersed repeats, including a remarkable 105-kb forward repeat implicated in genome expansion via repeat-mediated recombination. Selective pressure analysis indicated predominant purifying selection across PCGs, ccmBas showing signatures of positive selection. Phylogenomic reconstruction robustly placed <i>Cyclocarya paliurus</i> within the Juglandaceae, while collinearity analysis revealed extensive genomic rearrangement relative to <i>Juglans</i> species. Furthermore, 30 homologous fragments and two intact genes (<i>nad1</i>, <i>matR</i>) were identified between the mitogenome and plastome, evidencing intracellular gene transfer. This study provides the first comprehensive characterization of the <i>Cyclocarya paliurus</i> mitochondrial genome, offering essential genomic resources for molecular marker development, phylogenetic studies, and elucidation of bioactive metabolites pathways.</p>

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Assembly and phylogenetic analysis of the mitochondrial genome of the Cyclocarya paliurus

  • 期刊论文

  • 发表日期：

    2026年6月16日

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  • Hanjie Chen,
  • Zhenglong Zhao,
  • Linxin Shen,
  • Meilan Yu

摘要

Cyclocarya paliurus, a rare Chinese endemic known as the “sweet tea tree,” possesses significant hypoglycemic properties and holds dual status as both a traditional health beverage and an approved novel food ingredient. Despite extensive phytochemical research, its complete mitochondrial genome remained uncharacterized. This study reports the first assembly and annotation of the Cyclocarya paliurus mitogenome using PacBio HiFi long-read sequencing. The mitochondrial genome consists of two circular molecules (398,659 bp and 355,751 bp), featuring a stable GC content (~ 45%) and ranking among the largest within the Juglandaceae. Genome annotation revealed 75 functional genes, including 45 PCGs, 26 tRNAs, and 3 rRNAs. With the elevated tRNA count suggesting specialized roles in translational regulation. Predicted RNA editing identified 616 sites, predominantly causing hydrophilic-to-hydrophobic substitutions, while codon usage analysis confirmed a strong A/T-end bias. Repetitive sequence analysis uncovered abundant SSRs and dispersed repeats, including a remarkable 105-kb forward repeat implicated in genome expansion via repeat-mediated recombination. Selective pressure analysis indicated predominant purifying selection across PCGs, ccmBas showing signatures of positive selection. Phylogenomic reconstruction robustly placed Cyclocarya paliurus within the Juglandaceae, while collinearity analysis revealed extensive genomic rearrangement relative to Juglans species. Furthermore, 30 homologous fragments and two intact genes (nad1, matR) were identified between the mitogenome and plastome, evidencing intracellular gene transfer. This study provides the first comprehensive characterization of the Cyclocarya paliurus mitochondrial genome, offering essential genomic resources for molecular marker development, phylogenetic studies, and elucidation of bioactive metabolites pathways.