The complete chloroplast genome of Rhododendron ambiguum and comparative genomics of related species

<i>Rhododendron</i> Linnaeus, 1753, the largest genus of woody plants in the Northern Hemisphere, includes some of the most significant species in horticulture. <i>Rhododendronambiguum</i> Hemsl, 1911, a member of subsection Triflora Sleumer 1947, exemplifies typical alpine <i>Rhododendron</i> species. The analysis of the complete chloroplast genome of <i>R.ambiguum</i> offers new insights into the evolution of <i>Rhododendron</i> species and enhances the resolution of phylogenetic relationships. This genome is composed of 207,478 base pairs, including a pair of inverted repeats (IRs) of 47,249 bp each, separated by a large single-copy (LSC) region of 110,367 bp and a small single-copy (SSC) region of 2,613 bp. It contains 110 genes: 77 protein-coding genes, 29 tRNAs, four unique rRNAs (4.5S, 5S, 16S, and 23S), with 16 genes duplicated in the IRs. Comparative analyses reveal substantial diversity in the <i>Rhododendron</i> chloroplast genome structures, identifying a fourth variant pattern. Specifically, four highly divergent regions (<i>trnI-rpoB</i>, <i>ndhE-psaC</i>, <i>rpl32-ndhF</i>, <i>rrn16S-trnI</i>) were noted in the intergenic spacers. Additionally, 76 simple sequence repeats were identified. Positive selection signals were detected in four genes (<i>cemA</i>, <i>rps4</i>, <i>rpl16</i>, and <i>rpl14</i>), evidenced by high Ka/Ks ratios. Phylogenetic reconstruction based on two datasets (shared protein-coding genes and complete chloroplast genomes) suggests that <i>R.ambiguum</i> is closely related to <i>R.concinnum</i> Hemsley, 1889. However, the phylogenetic positions of subsection Triflora Pojarkova, 1952 species remain unresolved, indicating that the use of complete chloroplast genomes for phylogenetic research in <i>Rhododendron</i> requires careful consideration. Overall, our findings provide valuable genetic information that will enhance understanding of the evolution, molecular biology, and genetic improvement of <i>Rhododendron</i> spieces.