Exploring the chloroplast genomics, comparative analysis, evolution, and phylogenetic relationships of Phylica pubescens (Rhamnaceae) in the Cape Flora

•The first complete chloroplast genome of phylica genus (Phylica pubescens) was sequenced.•Several unique chloroplast genome characters in phylica pubescens and its closely related rhamnaceae species were identified to explore evolutionary pattern.•15 highly variable regions have been identified, which could be useful for phylogenetic analysis.•Based on complete chloroplast genomes, the phylogenetic tree of rhamnaceae was reconstructed. Phylica pubescens is closely related to spyridium species.•These findings provide insights into the evolutionary history of phylica pubescens and its relationship to other rhamnaceae species. Phylica (Rhamnaceae) plants are mainly distributed in southern Africa and nearby islands. They play a crucial role in studying diversification rates, climate change, and vegetation evolution in the Cape Flora. However, there have been no reports on the complete chloroplast genome of Phylica species, which is essential for investigating evolution and phylogenetic relationships. Herein, we sequenced the complete chloroplast genome of Phylica pubescens and conducted a comparative analysis with 12 Rhamnaceae species. The chloroplast genome size of Phylica pubescens was 161,187 bp, similar to that of other Rhamnaceae species. The absence of infA and psbL genes in certain Rhamnaceae species, compared to Phylica pubescens, has no apparent impact on these species. Positive selection has been observed in the rpl32, psbK, and psbH genes of Rhamnaceae species. Some highly variable regions (trnH-GUG–psbA, trnK-UUU–rps16, rps16–trnQ-UUG, trnS-GCU–trnG-UCC, trnR-UCU–atpA, atpH–atpI, trnC-GCA–petN, trnT-GGU–psbD, psbZ–trnG-GCC, trnT-UGU–trnL-UAA, ndhC–trnV-UAC, accD–psaI, petA–psbJ, ndhF–rpl32, and rpl32–trnL-UAG) were identified, which might be useful for phylogenetic analysis. Based on complete chloroplast genomes for the greatest number of species, the phylogenetic tree of the Rhamnaceae was reconstructed. Phylica pubescens displayed a close phylogenetic relationship with Spyridium species. This study provides valuable information regarding the complete chloroplast genome of Phylica pubescens and its comparative analysis with other Rhamnaceae species. These findings enhance our knowledge of the evolution within the Rhamnaceae family and shed light on the relationships between Phylica pubescens and closely related taxa.