- Qiang Li: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China. ORCID
The genus (Primulaceae) comprises more than 500 species, with 300 species distributed in China. The contradictory results between systematic analyses and morphology-based taxonomy make taxonomy studies difficult. Furthermore, frequent introgression between closely related species of can result in non-monophyletic species. In this study, the complete chloroplast genome of sixteen subsp. individuals were assembled and compared with 84 accessions of 74 species from 21 sections of the 24 sections of the genus in China. The plastome sizes of subsp. range from 153,584 bp to 154,028 bp. Genome-wide variations were detected, and 1915 high-quality SNPs and 346 InDels were found. Most SNPs were detected in downstream and upstream gene regions (45.549% and 41.91%). Two cultivated accessions, ZP1 and ZP2, were abundant with SSRs. Moreover, 12 SSRs shared by 9 accessions showed variations that may be used as molecular markers for population genetic studies. The phylogenetic tree showed that subsp. cluster into two independent clades. Two subspecies have highly recognizable morphological characteristics, isolated geographical distribution areas, and distinct phylogenetic relationships compared with subsp. . We elevate the two subspecies of to separate species. Our phylogenetic tree is largely inconsistent with morphology-based taxonomy. Twenty-one sections of were mainly divided into three clades. The monophyly of Sect. , Sect. , Sect. , Sect. , and Sect. are well supported in the phylogenetic tree. The Sect. , Sect. , Sect. , Sect. , Sect. , Sect. , Sect. , and Sect. are not a monophyletic group. The possible explanations for non-monophyly may be hybridization, polyploidization, recent introgression, incorrect taxonomy, or chloroplast capture. Multiple genomic data and population genetic studies are therefore needed to reveal the evolutionary history of . Our results provided valuable information for intraspecific variation and phylogenetic relationships within .