Organelle genomes reveal adaptive evolution and phylogenetic position of the endangered Primula mallophylla

Wenqiao Li¹Le Wang¹Youwei Zuo¹Huan Zhang¹Xiao Zhang¹Lingxiang Yang²Jiabin Zhang¹Fengyuan Zheng¹Hongping Deng^1*

• ¹Southwest University, Chongqing, China
• ²Administration Center of Chongqing Dabashan National Nature Reserve, Chongqing, China

Species of Primula section Proliferae are predominantly distributed in alpine environments above 2,000 meters and represent an important group for studying environmental adaptation and phylogenetic evolution. Primula mallophylla, holds important ecological, ornamental, and conservation value. However, genomic resources for this species remain unavailable, hindering further research on its genetic evolution and conservation strategies. In this study, we report for the first time the complete mitochondrial and chloroplast genomes of P. mallophylla, and conduct a comprehensive analysis of their structural characteristics and evolutionary dynamics. The results show that both the mitochondrial and chloroplast genomes exhibit typical master circular structures, with sizes of 340,219 bp and 150,733 bp, respectively. The mitochondrial genome has more abundant repetitive sequences and has undergone genomic rearrangements. There are only 9 MTPTs between mitochondria and chloroplasts, totaling 2,028 bp. In the regulation of mitochondrial genome expression, we predicted 475 RNA editing sites, with ccmB and mttB showing the highest potential editing frequencies. We found that P. mallophylla exhibits similar codon usage bias to most plants, and based on ENC-GC3s analysis, some genes appear to be under natural selection. Chloroplast genes rpl2, rpl22, rbcL, and ndhB exhibit branch-specific positive selection in Primula, reflecting adaptive evolution of photosynthesis and protein synthesis functions in high-altitude environments. On a large scale, the Primulaceae are most closely related to the Ebenaceae. The phylogenetic tree derived from the chloroplast genome showed that sect. Proliferae was not a monophyletic group, and P. stenodonta is a sister species to P. mallophylla. The results provide important support for further revealing the adaptive evolutionary process of Primula, clarifying the phylogenetic relationships, and formulating conservation strategies.