Comparative Transcriptomic Analysis Reveals Convergent Adaptation Mechanisms of Two Alpine Plants on the...

We used comparative transcriptome analysis to reveal convergent adaptations in two alpine plants. Firstly, the convergently expanded gene families were enriched in plant-pathogen interactions and secondary metabolism-related pathways, while the convergently contracted gene families were enriched in monoterpene and diterpene biosynthesis pathways. This suggested that there was a convergent growth-defense trade-off between the two alpine plants in adapting to the environment of Qinghai-Tibet Plateau (QTP). Secondly, the differentially expressed genes (DEGs) of P. pectinatus and B. bungei were significantly enriched in the photosynthesis-related pathway, and most DEGs of the LHC multifamily showed a significant trend of down-regulated expression. These results suggested that both alpine plants can converge to increase the energy dissipation rate or decrease the light energy absorption efficiency by down-regulating the expression of photosynthesis-related genes to cope with the intense light environment of the QTP. Thirdly, the comparative genomic analysis and population-level Fst analysis showed that genes involved in nucleic acid repair and secondary metabolites were positively selected and rapidly selected, which facilitated the plant's resistance to DNA damage caused by intense UV radiation and low temperature. Finally, analysis of positive selection and differential expression showed that genes related to secondary metabolites synthesis and nucleic acid repair were positively selected, and genes related to photosynthesis were down-regulated, indicating that genetic adaptation and gene expression regulation were mutually coordinated processes in the adaptation to extreme environments. Taken together, this study provided valuable insights into the convergent adaptation of different plants to the unique conditions of QTP.