Comparative Chloroplast Genomics And Phylogenetics Of The Genus Cilantro In Chin

Hydrocotyle L.is a cosmopolitan genus and belongs to Araliaceae.It was widely used in ornamental,edible and medicinal plants in China,which has important economic value.Previous molecular phylogenetic studies have revealed that Hydrocotyle is a monophyletic group,but only a few species are involved in China.As a result,the relationships among Hydrocotyle species in China remain unclear.In this study,the complete chloroplast(cp)genomes of 13 species of Hydrocotyle were sequenced utilizing the Next Generation Sequencing(NGS).Hydrocotyle chloroplast genomes structure,codon bias,and repeat sequences were investigated.Combing with 4 published cp genomes,a comparative genomic analysis among Hydrocotyle was conducted.Based on the cp genome data,the phylogenetic relationships among Hydrocotyle were reconstructed.The main results of this study are as follows.1)The length of the chloroplast genomes ranged from 152,659 to 153,669 bp,with a circular quadripartite structure that included a large single-copy region(LSC),a small single-copy region(SSC),and two inverted repeat sections(IR).A total of 114 unique genes were encoded,including 80 protein-coding genes,30 t RNAs,and four r RNAs genes.In addition,2,241 SSR sequences were identified,most of which were single nucleotide repeats,and 404 long repeats were detected,most of which were forward repeats and palindrome repeats.The codon usage bias of Hydrocotyle was the same,showing a preferred usage of codons ending with A/T base,and a non-standard start codon(GTG)was found in rps19 and ndh D gene.2)The chloroplast genomes were found to be highly conserved in comparative genomic investigations.Other than H.calcicola,there was no significant variation in expansion and contraction of the IR region.The chloroplast genomes of Hydrocotyle have no rearrangement or inversion events,according to collinear relationship analysis.The two IR regions were more conservative than the LSC and SSC regions,and the coding region was more conservative than the noncoding region,according to a comparison of sequence identity plots.Genetic distance analysis revealed that cp genomes of Hydrocotyle had little difference in genetic distance and low level of sequence differentiation.Sliding window analysis was used to screen out 11 highly variable fragments,including rpl22-rps19,pet N-psb M,trn T-UUC-trn E-GGU,psa B,ycf3-trn S-GGA,ndh C-trn V-UAC,pet A-psb J,psb E-pet L,rpl16-intron,ndh F-rpl32 and ycf1.3)Based on seven chloroplast genome data sets(CP,LSC,SSC,IR,CDS,NCR,and H-V),the phylogenetic tree of Hydrocotyle was constructed using maximum likelihood(ML)and Bayesian influence(BI).The phylogenetic trees based on different methods and data sets showed relatively consistent topology.All phylogenetic trees showed that Hydrocotyle was a monophyletic group.The phylogenetic tree constructed by the IR region showed a lower relative resolution than that of the phylogenetic trees constructed by the other six data sets.Phylogenetic analysis results show that chloroplast genome data can effectively solve the phylogenetic relationships among the species of Hydrocotyle.