Comparative analysis of the chloroplast genomes of Rhododendron capitatum, R. przewalskii, and Rhododendron species

Rhododendron capitatum and R. przewalskii are ornamental flowers and medicinal plants. The chloroplast genomes of R. capitatum and R. przewalskii have been sequenced using Illumina HiSeq 4000 platform to explore the genetic structure and evolution features. After assembly and annotation, comparative genomic analysis and phylogenetic analysis of the chloroplast genomes of R. capitatum and R. przewalskii were analyzed and compared with those of other Rhododendron species. The results were as follows: (1) The chloroplast genomes of R. capitatum and R. przewalskii exhibited a typical quadripartite structure, including a large single copy region (105 990, 109 191 bp), a small single copy region (2 617, 2 606 bp), and a pair of inverted repeat regions (45 825, 47 516 bp). And the two Rhododendron species chloroplast genomes were 200 257 bp and 206 829 bp in length, respectively. (2) In addition, the 263 SSRs were detected in the chloroplast genomes of R. capitatum and R. przewalskii, most of which had A/T base preference; the codons preferred ending in A/U. (3) The chloroplast genomes of Rhododendron species exhibit structural variation such as gene loss and genomic rearrangement. The study enriches the genomic resources of Rhododendron species and provides the theoretical reference for resource exploitation, genetic evolution, breeding, and phylogeny of R. capitatum and R. przewalskii.