Edaphic specialization—the adaptation of plants to unique or extreme soil environments—yields critical insights into ecological differentiation and the evolutionary mechanisms driving biodiversity, yet its genomic basis remains poorly understood.

Primulina, a genus of Gesneriaceae comprising over 200 species endemic to extreme soils, is predominantly calciphilous (limestone-adapted); a small number of species have independently adapted to Danxia or acidic soils, making it an exceptional model for mechanistic dissection.

A research team from the South China Botanical Garden of the Chinese Academy of Sciences (CAS), recently assembled seven genomes and constructed a Primulina pan-genome encompassing nine species from karst, Danxia, and acidic soil habitats. Comparative analyses reveal that karst-adapted species possess smaller genomes than non-karst counterparts, providing strong support for the nitrogen limitation hypothesis. Two lineage-specific whole-genome duplications (WGDs) were found to exhibit biased duplicate loss in large gene families, while preferentially retaining transcription factors—indicating the combined action of adaptive and nonadaptive forces.

Pan-genome analyses identified ion channel and transporter genes enriched in variant hotspots and under positive selection in karst lineages. Candidate genes for drought and salt stress tolerance include ABC transporters and ion channels. Notably, an ABC transporter gene shows signatures of positive selection in karst species and unique structural variation in non-karst species.

Collectively, this study demonstrates that genome downsizing, biased post-WGD retention patterns, and the evolution of ion transport pathways shape plant adaptation to extreme soils. The Primulina pan-genome serves as a valuable resource for dissecting the mechanisms underlying edaphic specialization.

The findings were recently published in Cell Reports. This work was supported by the Guangdong Flagship Project of Basic and Applied Basic Research, the National Natural Science Foundation of China, and the CAS Youth Innovation Promotion Association.