Adaptive Evolution Of Photosynthetic Genes In Dendrobium Plants Based On Chloroplast Genome And Transcriptome

Dendrobium is the second largest genus of Orchidaceae.It is a typical epiphytic orchid,usually attached to rocks or tree trunks,and has high ornamental value.In addition,most of the Dendrobium species can be used medicinally,with special effects such as nourishing yin and promoting body fluid,lowering blood sugar,and prolonging life.About 100 species of Dendrobium in China(about 80 species on the Chinese mainland and 20 species in Taiwan),with a wide geographical distribution and a large altitude distribution span.In order to adapt to its epiphytic habits and different habitats,multiple CO₂ fixation pathways,i.e.,C3 pathway,weak-crassulacean acid metabolism(CAM)and strong-CAM,have presented during their evolutionary radiation.It is obvious that Dendrobium species is an excellent model for the parallel evolution of CAM.So far,researches on the differences in photosynthesis among Dendrobium species in China are still scarce,especially the molecular mechanism of CAM.Therefore,this study is the first to carry out the following work from the perspective of the complete chloroplast genomes and transcriptome sequencing technology:The eight complete plastome sequences were employed of the Dendrobium species of China(D.officinale,D.nobile,D.thyrsiflorum,D.terminale,D.acinaciforme,D.chrysotoxum,D.primulinum,D.longicornu).The results showed that the chloroplast genomes of Dendrobium were conserved in terms of gene structure,composition and number.Significant contraction or expansion occurred in the IR region.This study further uses the Maximum likelihood(ML)and Bayesian inference(BI)analysis was performed for the complete plastome sequences.According to BEAST analysis,we deduce the interspecific divergence of the two major branches between Dendrobium Asia and Dendrobium Australia to be in the late Tertiary(23.20–26.25 Ma).They evolved rapidly to adapt to the environmental changes.Comparative Genomics analysis showed that the Insertion/Deletion is inconsistent in different photosynthetic pathways of Dendrobium species.At the same time,based on the site model,the selection pressure analysis of photosynthesis related genes of Dendrobium species showed that a total of 11 genes were under nature selection.The branch-site model also identified 6 genes and 27 nature selection sites,indicating that the adaptive evolution of chloroplast-encoded photosynthetic genes is related to the transformation of the photosynthetic pathway of Dendrobium species.This study performed transcriptome sequencing analysis on representative species of Dendrobium with different photosynthetic pathways selected in the previous study(A total of 48 samples,each of which was sampled during the day/night,and each sample was repeated three times).Based on the reference pair of the third-generation Dendrobium officinale genome,the photosynthesis related genes were assembled.It was found that a total of 51 genes involved in the photosynthetic pathway ko00195,ko00196,and ko00710 were affected by nature selection,which shows that nuclear-encoded photosynthetic related genes have adaptive evolution in different photosynthetic pathways.Therefore,the complete chloroplast genomes and transcriptomes of Dendrobium species were sequenced in this study,and we speculate that the changes in photosynthetic pathways of Dendrobium species in China were associated with the parallel evolution of photosynthetic related genes.In addition,counting the gene expression among different Dendrobium species and screening differentially expressed genes lays a foundation for clarifying the screening of essential enzyme genes in the synthesis pathways of necessary medicinal active ingredients among various species.