Phylogeny and comparative chloroplast genomics reveal a rare new short-styled homostylous species of Primula (Primulaceae) from southwestern China.

Based on comparative chloroplast genomes (cp genomes) and phylogenetic analyses integrated with morphological evidence, this study investigated the taxonomic status and phylogenetic relationships of an extremely rare short-styled homostylous lineage of Primula from southwestern China, providing new molecular insights into the delimitation of this complex group. Complete cp genomes were sequenced and comparatively analyzed for one putative new taxon, Primula panzhouensis, and 15 representative samples within Sect. Petiolares from southwestern China. The cp genome characteristics, simple sequence repeat (SSR) patterns, codon usage bias, inverted repeat (IR) boundary variations, and nucleotide diversity patterns were systematically evaluated. Maximum likelihood (ML) and Bayesian inference (BI) analyses were conducted based on complete cp genome sequences, and an integrative taxonomic assessment was performed by combining cp genomic evidence with morphological comparisons. All 16 cp genomes exhibited a typical quadripartite structure, with genome sizes ranging from 151,076 to 153,420 bp. The overall cp genome structure and gene composition were highly conserved, although interspecific variations were detected in IR boundary regions, SSR distributions, and highly variable regions, including trnH-psbA and ycf1. The sequenced cp genome of P. panzhouensis exhibited several distinctive structural features and sequence variation patterns compared with closely related taxa. ML and BI analyses consistently recovered P. panzhouensis as a distinct cp lineage within Sect. Petiolares with strong support. Morphological comparisons further demonstrated that P. panzhouensis possesses the short-styled homostyly trait and can be distinguished from related taxa by differences in floral style structure, corolla morphology, scape length, and leaf characteristics. Integrating cp genomic evidence, phylogenetic relationships, and morphological traits, our results support the recognition of P. panzhouensis as a distinct taxonomic entity, which is herein described as a new species, Primula panzhouensis Z.K.Wu, sp. nov. This study demonstrates that comparative cp genomics integrated with phylogenetic analyses can effectively assist in resolving lineage relationships and taxonomic boundaries in complex groups of Primula. It also identifies an extremely rare short-styled homostylous species, providing valuable material for further investigating the evolution of floral diversity and its potential evolutionary significance in Primula.