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

Abstract

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 (Pn), 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 (JSBs) 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.

Comparative Analysis of Luisia (Aeridinae, Orchidaceae) Plastomes Shed Light on Plastomes Evolution and Barcodes Investigation

“…All Luisia plastomes possess the typical quadripartite structure of angiosperm plastomes, consisting of a pair of IRs ranging from 25,195 to 25,460 bp, separated by the LSC (85,208-85,953 bp) and SSC (10,,412 bp) regions (Figure 1). The plastome size (ranging from 146,243 to 147,430 bp) and GC content (36.6%) were similar to those observed in other Orchidaceae lineages [47,48]. Additionally, there were no rearrangements among Luisia plastomes detected by the collinearity analysis (Figure 2).…”

Genome-wide identification and characterization of TCP gene family in Dendrobium nobile and their role in perianth development

“…This assumption is also supported by the GO prediction ( Figure 7A ). Dendrobium orchids have developed multiple photosynthetic pathways, as the CAM pathway has evolved at least eight times independently ( Li et al., 2019 ; Xue et al., 2023 ). Thus, the promoters of DnTCP genes contain many cis-acting elements associated with light sensitivity.…”

Genome-Wide Identification and Analysis of TCP Gene Family among Three Dendrobium Species

“…Compared with the diversified habitat of D. officinale and D. nobile , which have a varied environment, D. chrysotoxum species are mainly distributed in warm regions. There are different photosynthesis pathways among the three species, whereby D. officinale and D. nobile are facultative CAM plants, while D. chrysotoxum is a C3 plant [ 41 ]. Considering the diversified habitats, photosynthesis pathways, and the critical functions of CIN genes, we suggest that the loss of CIN genes in D. chrysotoxum led to a compact TCP gene family of D. chrysotoxum , resulting a diversified TCP gene family among Dendrobium species.…”

“…are crassulacean acid metabolism (CAM) plants; D. nobile , D. officinale , and Dendrobium hercoglossum Rchb. f. are recognized as C3-CAM plants [ 41 ]. The higher expression of DoTCP genes may improve the response of D. officinale to light stress by changing the photosynthesis pathway from C3 to CAM upon exposure to light stress.…”