Characteristics, comparative genomics, and phylogenetic analysis of the chloroplast genome of <i>Rosaplatyacantha</i>

Background Rosa platyacantha is a rose species endemic to the high-altitude regions of Xinjiang in China. To date, no complete chloroplast genome has been reported for this species, limiting our understanding of its genomic characteristics and phylogenetic relationships within the genus Rosa . Methods This study employed Sequencing by Synthesis (SBS) technology to achieve the first complete sequencing, assembly, and annotation of the R. platyacantha chloroplast genome. Comparative genomics and phylogeny analyses were then conducted using this data alongside chloroplast genome data from other Rosa species. Results The chloroplast genome of R. platyacantha spans 157,133 bp, and it annotates 132 genes and has a total guanine cytosine (GC) content of 37.21%. Fifty-one simple sequence repeat (SSR) loci were identified, predominantly adenine/thymine (A/T)-type mononucleotide repeats. Codon usage preference analysis revealed a marked bias towards synonymous codons ending in adenine/uracil (A/U). Compared to closely related species, R. platyacantha exhibited higher nucleotide diversity (Pi) in non-coding regions and the large single copy (LSC) and small single copy (SSC) region. Potential adaptive hot spots were identified at ycf3-trnS -GCU (Pi = 0.29005), trnC -GCA, trnT -UGU, and trnV -UAC. Rose genus chloroplast genomes are generally conserved, with most species exhibiting identical inverted repeat regions a and b (IRa and IRb) lengths. However, only R. acicularis shows a 62 bp difference, and the associated fragment length of the duplicated gene ycf1 varies between species from 1,108 to 1,117 bp. Phylogeny analysis revealed that R. platyacantha did not cluster with the sympatric R. fedtschenkoana . This finding confirms their distant evolutionary relationship at the genome level, providing new insights into the evolutionary and dispersal pathways of Rosa species within the unique habitats of northwest China.