Phylogeny And Environmental Adaptation Evolution Analysis Of Hildenbrandia

Hildenbrandia is at the base of the evolutionary relationship of the freshwater red algae,and the study of its phylogenetic relationship is of great help to the exploration of the whole evolutionary relationship of the freshwater red algae.In this study,morphological observation was made on Hildenbrandia jigongshanensis from Niangziguan,Yangquan,Shanxi Province,and then assembled and annotated the chloroplast genome on the basis of sequencing.The chloroplast genomic characteristics such as genome length,GC content,and coding content were analyzed based on the genomic heat map of the Bayesian tree constructed with 34 other related red algae species(Hildenbrandia contains 4 species).Synteny alignment with Hildenbrandia rivularis and Hildenbrandia rubra was performed to analyze their gene rearrangement.Based on neighbor-joining method,Bayesian method and maximum likelihood method,a joint phylogenetic tree was constructed.At the same time,different datasets were formed by rearrangement and removal according to the GC-heterogeneity of loci.Phylogenetic trees based on nine datasets were constructed to compare the phylogenetic results and to analyze the phylogenetic relationships between H.jigongshanensis and other species of Rhodophyta.Basepair substitution rates of different coding genes were calculated to analyze their potential as molecular markers in phylogenetic studies of red algae.Furthermore,the adaptive evolution of 62 common coding genes was analyzed by using branch model,site model and branch-site model.The results showed that the algal body color of H.jigongshanensis used in this experiment was purple red,the cells were nearly square,the diameter was about50-200 mm,the width was 9.8-19.6μm,and the length was 9.9-10.4μm.After assembly of high-throughput sequencing data,the chloroplast genome showed a typical circular,with a length of 178406 bp and a GC content of 30.81%,encoding 227 genes.The chloroplast genome size of H.jigongshanensis is the smallest in the Hildenbrandiophycidae.The GC content is lower than that of H.rivularis and H.rubra,but slightly larger than that of Apophlaea sinclairii(the same class as Hildenbrandia),and the length ratio of CDS and r RNA is higher than that of other three species in Hildenbrandiophycidae.The collinearity analysis showed that the chloroplast genome modules of H.jigongshanensis and H.rivularis had strong collinearity,but there were two rearrangements in the chloroplast genome compared with the H.rubra.Phylogenetic results from different methods showed that all trees consist of three branches: the Florideophyceae,the Bangiophyceae and the Compsopogonophyceae.The phylogenetic relationships of Hildenbrandiophycidae,Nemaliophycidae and Corallinophycidae were stable,while the phylogenetic relationships within Rhodymeniophycidae were different under different phylogenetic models.All phylogenetic trees supported the convergence of H.jigongshanensis and H.rivularis,and the support rate was very high,indicating that H.jigongshanensis,as a freshwater red algae,had a close relationship with H.rivularis.The Ka/Ks was calculated to detect the basepair substitution rates.It was found that the Ka/KS of all genes was less than 0.5,while the basepair substitution rates was high in the ribosomal protein LSU gene,which had a faster rate of evolution.The results of adaptive evolution analysis showed that no statistically significant positive selection sites were detected for protein-coding genes in chloroplast genome of Hildenbrandia,indicating that Hildenbrandia was under strong purification selection pressure,which maybe caused by its special requirements for habitat and long-term asexual reproduction.In this study,we assemble the chloroplast genome of H.jigongshanensis,and construct phylogenetic relationships of H.jigongshanensis based on different evolutionary models,which provides a theoretical basis for the origin and evolution of the Hildenbrandia.The comparison of basepair substitution rates in different genes could provide molecular markers for species identification and phylogenetic analysis of Hildenbrandia in future.The statistical analysis of positive selection sites provided a theoretical basis for further exploring the adaptive evolution of this group and the environment.