| Calypsoinae belongs to Epidendroideae of Orchidaceae,with 79 species belonging to 12 genera,and is a widely distributed taxa in the northern hemisphere.According to the different utilization of carbon sources,there are two trophic types of orchids,autotrophic and heterotrophic.Therefore,it is a good material to study the chloroplast genome evolution of different trophic types of orchids.This study used three generation of sequencing technology assembly annotation heterotrophic Danxiaorchis yangii chloroplast genome,and the NCBI download published Calypsoinae chloroplast genome data.Using bioinformatics,system development,differentiation time estimation,the ancestors of reconstruction and diverse methods of velocity analysis,probes into the Calypsoinae with nutrient transformation of chloroplast genome evolution model and spatio-temporal evolutionary relation.The main results are as follows:1.Characteristics of Chloroplast Genome of Danxiaorchis yangii: The total length of the chloroplast genome was 95,156 bp,encoding a total of 79 different genes.Respectively,the ndh dehydrogenase complex genes were all lost.There are 8,728 pairs of codon in the chloroplast genome of Danxiaorchis yangii,and the codon preference ending in A/U is preferred.The ENC-plot analysis showed that the codon preference in the chloroplast genome of Danxiaorchis yangii is mainly affected by the selection pressure.A total of 27 SSRs were detected in the genome,and most of them were located in the non-coding region(60%).Most of the repeats were composed of single base and showed strong A and T bias in composition.2.Characteristics of Chloroplast Genomes of Different Lifestotypes of Calypsoinae:The size of the chloroplast genome of the subgroup Calypsoinae was 88-160 kb,and that of the genus Danxiaorchis was less than 100 kb,which was related to the significantly smaller LSC region of the genus Danxiaorchis.In terms of genome loss,both autotrophic and heterotrophic groups have gene loss phenomenon,mainly ndh family loss.Heterotrophic orchid gene loss is more serious,most of the genes related to photosynthesis have different degrees of deletion.In terms of genome structure,the chloroplast genome of autotrophic orchids is completely collinear without rearrangement and inversion,while heterotrophic orchids have rearrangement and inversion in the genus Danxiaorchis.3.The biogeography of the Calypsoinae: The Calypsoinae originated in Asia during the Eocene(32.13 Ma,95%HPD: 30.7-34.1).There were three subsequent dispersal events from Asia to North America,one from North America to Europe and one from Asia to Europe.The subgroups originated in tropical and subtropical evergreen broad-leaved forests,and then spread to subtropical,temperate and frigid zones several times.The genus Danxiaorchis originated from subtropical evergreen broad-leaved forest in Asia at 22.26 Ma.Two branches of the genus Corallorhiza appear in tropical and subtropical areas of North America at 13.95 Ma and 12.48 Ma.4.Diversification patterns of Calypsoinae: Diversification processes of Calypsoinae clades were different,with rapid diversification occurring around 28 Ma and a steady increase occurring at 20 Ma.The rate of net diversification of most genera of the whole subgroup was increasing,but the rate of net diversification of Danxiaorchis and Changnienia showed a decreasing trend.The extinction rate of Danxiaorchis showed an upward trend after 15 Ma,and the extinction rate of two branches of Corallorhiza was basically stable.According to the net diversity rate hypothesis,the species diversity of Corallorhiza was higher than that of Danxiaorchis. |
