Chloroplast genome comparison and phylogenomics of Androsace s.l., insight for the phylogenetic relationship of sect. Mirabiles

Androsace L. (Primulaceae) comprises approximately 120 Northern Hemisphere temperate species, with 73 species and 7 varieties native to China, of which at least 13 have ethnomedicinal value. Previous studies with limited loci left the generic circumscription of Androsace s.l. and the phylogenetic positions of Sect. Mirabiles unresolved. To clarify interspecific relationships, and identify variable markers for Androsace phylogeny studies, we sequenced, assembled, and annotated the chloroplast genomes of 31 Androsace species, 12 of which were selected for detailed comparative genomic analysis, combined with one Lysimachia species and one Primula species downloaded from NCBI to reconstruct a robust phylogeny of Androsace based on protein-coding genes. The chloroplast genomes of 12 Androsace species displayed a typical quadripartite structure from 147,325 to 153,359 bp in length. These genomes encoded 113–114 unique genes. Abundant palindromic repeats and A/T-rich SSRs were detected. We identified 12 highly variable regions as potential DNA barcodes. Although all genes experienced strong purifying selection, three out of eight genes assessed for selection harboured positively-selected sites. Phylogenomic analyses supported the recognition of Sect. Mirabiles and we propose transferring A. graceae to Sect. Samuelia given its close phylogenetic affinity to this section. Our results provide reliable plastid markers and phylogenetic evidence for taxonomic revision and evolutionary study of Androsace , and supply genomic references for subsequent medicinal resource exploitation.