Comparative chloroplast genomics reveal two new species of Primula sect. Auganthus (Primulaceae) from the karst regions of China: Primula shibingensis and P. longmenshanensis

Strong habitat heterogeneity in karst regions is widely considered a crucial mechanism underlying species differentiation, particularly for rapidly radiating groups such as the Primulaceae, where habitat heterogeneity readily facilitates species divergence and formation. During field investigations in Sichuan Province and Guizhou Province in southwestern China, we discovered two morphologically distinct populations of Primula . Their deeply lobed leaves and distinctly inflated calyces with a flattened base suggest that they belong to sect. Auganthus , yet their morphology is conspicuously different from all known species of this section, highlighting the urgent need for comparative chloroplast genome analyses to elucidate their phylogenetic relationships. Through morphological and comparative chloroplast genome analyses, we elucidated the phylogenetic relationships and revealed two new species. Combining morphological and comparative chloroplast genome analyses, we constructed a phylogenetic tree and performed comparative analyses using boundary contraction and expansion, mVISTA global comparison, and diversity site analysis. In the phylogenetic analysis, the two new species clustered together with all known species of sect. Auganthus . The IR region lengths of the two putative new species are 25,403 bp and 25,710 bp, respectively. A total of seven highly variable hotspots were detected in the diversity site analysis, with intergenic regions including psbI–trnS-GCU , trnS-GCU–trnG-UCC , trnT-GGU–psbD , as well as the genes accD and ycf1 , exhibiting high nucleotide diversity among species. Additionally, the two putative new species each possess distinct morphological characteristics. Based on morphological and phylogenetic evidence, both newly discovered species are recognized as new to science. They are named Primula longmenshanensis J.L.Gu & Z.K.Wu, sp. nov. and Primula shibingensis J.L.Gu & Z.K.Wu, sp. nov. according to their distribution localities. Their morphological comparisons with closely related species, distribution ranges, and conservation status are also provided in this paper.