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<p>This study reports for the first time the complete chloroplast genome sequence and genomic characteristics of <i>Rosa bella</i> from the northeastern Qinghai-Tibet Plateau. The genome size is 157,282&#xa0;bp, comprising a large single-copy region (LSC, 86,410&#xa0;bp), a small single-copy region (SSC, 18,790&#xa0;bp), and inverted repeat regions (IRa/IRb, each 26,041&#xa0;bp), with an overall GC content of 37.19%. A total of 133 genes were assembled, comprising 8 rRNA genes, 37 tRNA genes, and 88 protein-coding genes, of which 20 contained introns. Sequencing identified 46 SSR loci, predominantly consisting of single-nucleotide repeats (93%), while trinucleotide repeats and longer sequences remain undetected. Codon usage exhibited a preference for A/U-termination (U-termination 51.72%, A-termination 41.38%). Comparative analysis of <i>R. bella</i> with ten other Rosaceae species published in NCBI revealed minimal variation in chloroplast genome size, ranging from 156,793 to 157,396&#xa0;bp. Nucleotide polymorphism analysis indicated higher variability in LSC region (Pi ≥ 0.2), whereas IRs regions exhibited lower variability (Pi &lt; 0.2). The phylogenetic tree revealed that <i>R.bella</i> and <i>R.kokanica</i> form distinct branches, potentially representing a sister relationship, with <i>R.acicularis</i> constituting a monophyletic clade. These findings elucidate their evolutionary position within the genus Rosa, laying the foundation for species identification and molecular breeding.</p>

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Evolutionary insights from the Rosa bella chloroplast genome: codon usage bias, nucleotide diversity, and phylogeny

  • 期刊论文

  • 发表日期：

    2026年2月24日

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  • Gang Lu,
  • Mengmeng Yu,
  • Guoqin Han,
  • Penghui Yang,
  • Fazu Xu,
  • Youju Wang,
  • Xiaoqing Zhang,
  • Tingliang Xu,
  • Fashou Liu,
  • Yihui Liu

摘要

This study reports for the first time the complete chloroplast genome sequence and genomic characteristics of Rosa bella from the northeastern Qinghai-Tibet Plateau. The genome size is 157,282 bp, comprising a large single-copy region (LSC, 86,410 bp), a small single-copy region (SSC, 18,790 bp), and inverted repeat regions (IRa/IRb, each 26,041 bp), with an overall GC content of 37.19%. A total of 133 genes were assembled, comprising 8 rRNA genes, 37 tRNA genes, and 88 protein-coding genes, of which 20 contained introns. Sequencing identified 46 SSR loci, predominantly consisting of single-nucleotide repeats (93%), while trinucleotide repeats and longer sequences remain undetected. Codon usage exhibited a preference for A/U-termination (U-termination 51.72%, A-termination 41.38%). Comparative analysis of R. bella with ten other Rosaceae species published in NCBI revealed minimal variation in chloroplast genome size, ranging from 156,793 to 157,396 bp. Nucleotide polymorphism analysis indicated higher variability in LSC region (Pi ≥ 0.2), whereas IRs regions exhibited lower variability (Pi < 0.2). The phylogenetic tree revealed that R.bella and R.kokanica form distinct branches, potentially representing a sister relationship, with R.acicularis constituting a monophyletic clade. These findings elucidate their evolutionary position within the genus Rosa, laying the foundation for species identification and molecular breeding.