A complete chloroplast genome of a traditional Chinese medicine herb, , and phylogenomics of Rubiaceae.

UNLABELLED

Diels is endemic to southwestern China and belongs to the family Rubiaceae. It is used in traditional Chinese medicines. To enrich the genetic data and resolve Rubiaceae's phylogeny, we assembled a complete chloroplast (cp) genome of using Illumina HiSeq reads. The whole length of the cp genome was 154,866 bp. Annotation using PGA software found 113 genes, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. The large single-copy region was 84,717 bp, the inverted repeat B (IRa) region was 26,516 bp, the small single copy was 17,117 bp, and the inverted repeats B (IRb) region was 26,516 bp. Moreover, 64 SSRs were identified. Phylogenomic analysis using cp genomes of 109 Rubiaceae species found that is closely related to . Rubiaceae was separated into three subfamilies: Ixoroideae, Cinchonoideae, and Rubiodeae. The genus was not imbedded within the Spermacoceae alliance as reported in previous studies. Instead, it was imbedded within the Psychotrieae alliance. Divergence time estimation indicated that split from its relative around 1.25 million years ago. The assembled chloroplast genome in this study provided useful molecular information about the evolution of and was a basis for phylogenetic analyses of Rubiaceae.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-023-01302-y.