Scholarlink

<p>The genus <i>Curcuma</i> (Zingiberaceae) presents significant taxonomic challenges due to morphological convergence and a complex evolutionary history shaped by ancient hybridization and polyploidy. While complete chloroplast (cp) genomes offer valuable data for inferring maternal phylogenetic relationships within the five main <i>Curcuma</i> lineages, detailed characterization for many species is still needed. Here, we report the first complete cp genome of <i>Curcuma cochinchinensis</i>, a species belonging to the lineage <i>Pierreana</i>. The cp genome is 163,713&#xa0;bp long and exhibits a quadripartite structure with 113 unique genes (79 protein-coding genes, four ribosomal RNAs, and 30 transfer RNAs) and a GC content of 38.1%. Comparative analyses revealed high structural conservation across <i>Curcuma</i> species. However, specific non-coding regions (e.g., <i>psbK–psbI</i> and <i>rpoB–psbD</i> intergenic spacer) showed elevated nucleotide divergence, highlighting their potential for molecular marker development. Analysis of repetitive sequences and codon usage revealed patterns consistent with other Zingiberaceae cp genomes, including a predominance of AT-rich short simple repeats and palindromic repeats and a bias towards A/U-ending codons. Signals of positive selection were detected in 14 plastid genes, notably the mutation hotspots (<i>ycf1</i>, <i>ycf2</i>, <i>ndhF</i>, <i>matK</i>) and stress-response genes (<i>ndhB</i>, <i>ccsA</i>, <i>rpoC1</i>). Phylogenetic inference based on 79 cp protein-coding genes robustly places <i>C. cochinchinensis</i> in a monophyletic group with <i>C. singularis</i>, <i>C. xanthella,</i> and <i>C. pierreana,</i> confirming its maternal affinity with the <i>Pierreana</i> lineage. These findings offer important genomic insight into an underexplored lineage and contribute a valuable resource for future taxonomic, evolutionary, and conservation research within <i>Curcuma</i>.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

The complete chloroplast genome of Curcuma cochinchinensis Gagnep, 1907 (Zingiberaceae): insights into phylogeny and comparative genomics

  • 期刊论文

  • 发表日期：

    2025年12月10日

查看全文
  • Bao Ngoc Mach,
  • Hoang Danh Nguyen,
  • Minh Huy Nguyen,
  • Thi Thanh Nga Le,
  • Thanh Loan Nguyen,
  • Van Van Vu,
  • Thi Thu Hoai Nguyen,
  • Minh Thiet Vu

摘要

The genus Curcuma (Zingiberaceae) presents significant taxonomic challenges due to morphological convergence and a complex evolutionary history shaped by ancient hybridization and polyploidy. While complete chloroplast (cp) genomes offer valuable data for inferring maternal phylogenetic relationships within the five main Curcuma lineages, detailed characterization for many species is still needed. Here, we report the first complete cp genome of Curcuma cochinchinensis, a species belonging to the lineage Pierreana. The cp genome is 163,713 bp long and exhibits a quadripartite structure with 113 unique genes (79 protein-coding genes, four ribosomal RNAs, and 30 transfer RNAs) and a GC content of 38.1%. Comparative analyses revealed high structural conservation across Curcuma species. However, specific non-coding regions (e.g., psbK–psbI and rpoB–psbD intergenic spacer) showed elevated nucleotide divergence, highlighting their potential for molecular marker development. Analysis of repetitive sequences and codon usage revealed patterns consistent with other Zingiberaceae cp genomes, including a predominance of AT-rich short simple repeats and palindromic repeats and a bias towards A/U-ending codons. Signals of positive selection were detected in 14 plastid genes, notably the mutation hotspots (ycf1, ycf2, ndhF, matK) and stress-response genes (ndhB, ccsA, rpoC1). Phylogenetic inference based on 79 cp protein-coding genes robustly places C. cochinchinensis in a monophyletic group with C. singularis, C. xanthella, and C. pierreana, confirming its maternal affinity with the Pierreana lineage. These findings offer important genomic insight into an underexplored lineage and contribute a valuable resource for future taxonomic, evolutionary, and conservation research within Curcuma.