Comparison of chloroplast genomes of Calypsoinae species (Orchidaceae) living on different lifeforms

Abstract

Abstract Background The vast majority of angiosperms obtain carbon sources through photosynthesis, while a few Mycoeterotropic plants rely entirely on symbiotic fungi to provide nutrition. The origin and evolution of Mycoeterotropic plant has always been the focus of botanists. Calypsoinae, a common subfamily of Epidendroideae within Orchidaceae, possesses abundant variation in morphology and living habits. Such variation includes that between autotrophy and heterotrophy, a notable discernment that may be exploited to investigate the chloroplast genome evolution of different trophic types of orchids. In this study, the complete chloroplast genome of Danxiaorchis yangii, a heterotrophic orchid, was newly sequenced using illumina HiSeq X ten platform followed by de novo assembly. Moreover, we conducted comparative analysis on 25 Calypsoinae species’ complete chloroplast (CP) genomes, providing insight to explore the chloroplast genome evolution of non-autotrophic plants. Results The Danxiaorchis yangii CP genome size is 95,156 bp in length encoding a total of 79 different genes. The CP genomes of 25 Calypsoinae species are typically 88–160 kb in length, while that of the genus Danxiaorchis was typically less than 100 kb, which is consistent with the significantly smaller LSC region of the genus Danxiaorchis. In terms of genome loss, both autotrophic and heterotrophic groups have gene loss phenomena, mainly ndh family loss. Heterotrophic orchid gene loss is more serious, wherein most of the genes associated with photosynthesis have different degrees of deletion. The chloroplast genome of autotrophic orchids was completely collinear without rearrangement or inversion, contrasted with heterotrophic Danxiaorchis, which showed rearrangement and inversion. Conclusion This study reported the chloroplast genome sequence of D. yangii, and interpreted its structure and gene number of the chloroplast genome. In addition, by comparing the chloroplast genomes of autotrophic orchids and heterotrophic orchids in Calypsoinae, we found an interesting correlation between the nutrition mode and the chloroplast genome structure. The present study increases understanding of the the evolutionary relationships between heterotrophic orchid and autotrophic plants.