The climate changes promoted the chloroplast genomic evolution of Dendrobium orchids among multiple photosynthetic pathways

Dendrobium orchids have multiple photosynthetic pathways, which can be used as a model system for studying the evolution of crassulacean acid metabolism (CAM). In this study, based on the results of the net photosynthetic rates (P-n), we classified Dendrobium species into three photosynthetic pathways, then employed and compared their chloroplast genomes. The Dendrobium chloroplast genomes have typical quartile structures, ranging from 150,841-153,038 bp. The apparent differences in GC content, sequence variability, and IR junctions of SSC/IRB junctions (J(SB)s) were measured within chloroplast genomes among different photosynthetic pathways. The phylogenetic analysis has revealed multiple independent CAM origins among the selected Dendrobium species. After counting insertions and deletions (InDels), we found that the occurrence rates and distribution densities among different photosynthetic pathways were inconsistent. Moreover, the evolution patterns of chloroplast genes in Dendrobium among three photosynthetic pathways were also diversified. Considering the diversified genome structure variations and the evolution patterns of protein-coding genes among Dendrobium species, we proposed that the evolution of the chloroplast genomes was disproportional among different photosynthetic pathways. Furthermore, climatic correlation revealed that temperature and precipitation have influenced the distribution among different photosynthetic pathways and promoted the foundation of CAM pathway in Dendrobium orchids. Based on our study, we provided not only new insights into the CAM evolution of Dendrobium but also provided beneficial genetic data resources for the further systematical study of Dendrobium.

Automated summary

Based on the net photosynthetic rates, Dendrobium species were classified into three photosynthetic pathways, and their chloroplast genomes were compared. Significant differences were found in GC content, sequence variability, and IR junctions among different photosynthetic pathways. Phylogenetic analysis revealed multiple independent CAM origins in selected Dendrobium species. The occurrence rates and distribution densities of insertions and deletions varied among different photosynthetic pathways. Furthermore, the evolution patterns of chloroplast genes were diversified among three photosynthetic pathways in Dendrobium. Temperature and precipitation influenced the distribution of different photosynthetic pathways and promoted the formation of CAM pathway in Dendrobium orchids.