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<p><i>Paeonia suffruticosa</i> ‘Cun Song Ying’ is a rare Japanese horticultural cultivar with significant ornamental value, but its genomic characteristics and phylogenetic status remain unreported. This study reports the first complete chloroplast (cp) genome of <i>P. suffruticosa</i> ‘Cun Song Ying’ to fill the gap in its genomic and evolutionary research, aiming to provide a theoretical basis for peony cultivar identification, origin research, and breeding protection. High-throughput sequencing combined with bioinformatics tools was used for genome assembly, annotation, and comparative analyses with 15 related <i>Paeoniaceae</i> species. The cp genome of ‘Cun Song Ying’ was systematically characterized in terms of structural features, repetitive sequences, codon usage bias, and phylogenetic relationships. The 152,704&#xa0;bp cp genome has a typical quadripartite structure (large single-copy region (LSC): 84,365&#xa0;bp; small single copy region (SSC: 17,047&#xa0;bp; inverted repeat region (IR): 25,646&#xa0;bp × 2), encodes 138 genes, with 6 hypervariable regions, 43 repeat sequences, 73 simple sequence repeats (SSRs), A/U-preferred codons, and is sister to <i>P. suffruticosa</i> ‘Luo Yang Hong’ (BS = 100, PP = 1.00). This study enriches the chloroplast genomic resources of <i>Paeoniaceae</i>, clarifies the evolutionary characteristics and phylogenetic position of ‘Cun Song Ying’, and provides important genomic data support for peony cultivar identification, origin tracing, and genetic breeding.</p>

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The first chloroplast genome of rare Japanese peony Paeonia suffruticosa ‘Cun Song Ying’: comparative genomics and maternal origin insight

  • 期刊论文

  • 发表日期：

    2026年7月11日

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  • Wenzhen Cheng,
  • Conghao Hong,
  • Mingyu Li,
  • Changyong Gao

摘要

Paeonia suffruticosa ‘Cun Song Ying’ is a rare Japanese horticultural cultivar with significant ornamental value, but its genomic characteristics and phylogenetic status remain unreported. This study reports the first complete chloroplast (cp) genome of P. suffruticosa ‘Cun Song Ying’ to fill the gap in its genomic and evolutionary research, aiming to provide a theoretical basis for peony cultivar identification, origin research, and breeding protection. High-throughput sequencing combined with bioinformatics tools was used for genome assembly, annotation, and comparative analyses with 15 related Paeoniaceae species. The cp genome of ‘Cun Song Ying’ was systematically characterized in terms of structural features, repetitive sequences, codon usage bias, and phylogenetic relationships. The 152,704 bp cp genome has a typical quadripartite structure (large single-copy region (LSC): 84,365 bp; small single copy region (SSC: 17,047 bp; inverted repeat region (IR): 25,646 bp × 2), encodes 138 genes, with 6 hypervariable regions, 43 repeat sequences, 73 simple sequence repeats (SSRs), A/U-preferred codons, and is sister to P. suffruticosa ‘Luo Yang Hong’ (BS = 100, PP = 1.00). This study enriches the chloroplast genomic resources of Paeoniaceae, clarifies the evolutionary characteristics and phylogenetic position of ‘Cun Song Ying’, and provides important genomic data support for peony cultivar identification, origin tracing, and genetic breeding.