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<p><i>Rubus</i>, belonging to the Rosaceae family, is recognized for its considerable medicinal properties. However, the genus's extensive diversity renders traditional morphological classification and universal DNA barcoding methods inadequate for precise <i>Rubus</i> species identification. This study compared the complete chloroplast (cp) genomes of 29 <i>Rubus</i> species, including the newly sequenced <i>Rubus niveus</i>. Our results indicated a conserved quadripartite structure within the cp genomes, spanning a total length between 155,144 and 156,506&#xa0;bp, and encoding 112 genes: 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. We further explored codon preferences across these genomes. The study revealed a relatively uniform cp genome structure, gene content, and codon usage among the <i>Rubus</i> species. Simple sequence repeats (SSRs) varied from 58 to 80 in number. The analysis of nucleotide polymorphism pinned down nine regions of high variability (<i>rpl32</i>, <i>rpl16</i>, <i>ndhF</i>, <i>trnK-UUU-rps16</i>, <i>petN-psbM</i>, <i>petA-psbJ</i>, <i>rps16-trnQ-UUG</i>, <i>trnT-GGU-trnL-UAA</i>, and <i>rpl32-trnL-UAG</i>), which are promising markers for species identification and kinship studies. In addition, phylogenetic analysis across three datasets (cp genomes, coding sequences, and intergenic sequences) affirmed the monophyly of <i>Rubus</i> species. Notably, Sect. <i>Malachobatus</i> was characterized by unidirectional evolution, while Sect. <i>Idaeobatus</i> demonstrated a multilineage evolutionary pattern. These insights underscored the utility of cp genomes in elucidating the phylogenetic relationships within <i>Rubu</i>s, thereby offering a robust scientific basis for the phylogeny, classification, and species identification within the genus.</p>

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Comparative chloroplast genome analysis of the medicinal species in Rubus: Insights into genomic characterization and phylogenetic relationships

  • 期刊论文

  • 发表日期：

    2025年2月19日

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  • Jiayu Jiang,
  • Rui Tian,
  • Ruolan Wang,
  • Shuang Wang,
  • Dequan Zhang

摘要

Rubus, belonging to the Rosaceae family, is recognized for its considerable medicinal properties. However, the genus's extensive diversity renders traditional morphological classification and universal DNA barcoding methods inadequate for precise Rubus species identification. This study compared the complete chloroplast (cp) genomes of 29 Rubus species, including the newly sequenced Rubus niveus. Our results indicated a conserved quadripartite structure within the cp genomes, spanning a total length between 155,144 and 156,506 bp, and encoding 112 genes: 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. We further explored codon preferences across these genomes. The study revealed a relatively uniform cp genome structure, gene content, and codon usage among the Rubus species. Simple sequence repeats (SSRs) varied from 58 to 80 in number. The analysis of nucleotide polymorphism pinned down nine regions of high variability (rpl32, rpl16, ndhF, trnK-UUU-rps16, petN-psbM, petA-psbJ, rps16-trnQ-UUG, trnT-GGU-trnL-UAA, and rpl32-trnL-UAG), which are promising markers for species identification and kinship studies. In addition, phylogenetic analysis across three datasets (cp genomes, coding sequences, and intergenic sequences) affirmed the monophyly of Rubus species. Notably, Sect. Malachobatus was characterized by unidirectional evolution, while Sect. Idaeobatus demonstrated a multilineage evolutionary pattern. These insights underscored the utility of cp genomes in elucidating the phylogenetic relationships within Rubus, thereby offering a robust scientific basis for the phylogeny, classification, and species identification within the genus.