A Phylogenetic Study Of The Chloroplast Genome Of The Subgenus Salvia Asiatica In The Lamiaceae Family

Salvia subgenus Glutinaria(Raf.)G.X.Hu,C.L.Xiang & B.T.Drew belongs to the mint family(Lamiaceae).Lots of species in this genus can be used for ornamental,edible and medicinal purposes.Previous molecular phylogenetic studies have shown that the subg.Glutinaria is a monophyletic group,but species relationships within the genus are not clear.Chloroplast genome sequence is conserved,which is an important means to study phylogeny.In this study,complete chloroplast(cp)genome of 34 species of Salvia and 1 species of Lepechenia were sequenced using the Next Generation Sequencing(NGS).Chloroplast genome structures,codon bias and repeat sequences of 25 species of subg.Glutinaria were analyzed.Combing with published cp genomes,a comparative genomic analysis among subg.Glutinaria was conducted.Based on the cp genome data,phylogeny of subg.Glutinaria was reconstructed.The main results of this study are as follows.1)The cp genome structure of subg.Glutinaria is conservative,showing a typical circular quadripartite structure with a large single copy region(LSC),a small single copy region(SSC)and two inverted repeat regions(IRa,IRb).The length of cp genome ranged from 151,074 to151,678 bp,encoding 114 genes,including 80 protein coding,30 t RNAs and 4 r RNAs genes.The codon usage bias of subg.Glutinaria was the same,showing a preferred usage of codons ending with A/T base,and three non-standard start codons(GTG,TTG and CTG)were detected.In addition,4,273 SSR sequences were identified,most of which were single nucleotide repeats and1,246 long repeats were detected,most of which were forward repeats and palindrome repeats.2)Comparative genomics analyses showed that cp genomes of subg.Glutinaria is highly conserved.Except for S.przewalskii and S.mekongensis,the expansion and contraction of IR regions of other subg.Glutinaria did not show significant differences.Sequence identity plot comparison showed the two IR regions are more conservative than the LSC and SSC regions,and the coding region was more conservative than the noncoding region.Collinear relationship analysis suggested that there was no rearrangement or inversion events in the chloroplast genomes of subg.Glutinaria.Genetic distance analysis showed that cp genomes of subg.Glutinaria had little difference in genetic distance and low level of sequence differentiation.Seventeen highly variable fragments including rpl2-trn H-GUG,trn K-UUU,rps16-intron,atp F-intron,rpo B-trn C-GCA,psa A,ycf3,ndh J-ndh K,rbc L,rbc L-acc D,rps8-rpl14,trn N-GUU-ndh F,ndh F,ccs A-ndh D,ndh H,rps15-ycf1 and ycf1 were screened out by sliding window analysis.3)Based on the seven chloroplast genome datasets(CP,LSC,SSC,IR,CDs,NCR,H-V)of subg.Glutinaria,phylogenetic trees of subg.Glutinaria was constructed using maximum likelihood(ML)and Bayesian(BI).The phylogenetic trees based on different methods and data sets showed a similar topology: nine subgenera of Salvia can be identified,and subg.Glutinaria is a monophyletic group with S.sonchifolia and S.petrophila sister to the rest of subg.Glutinaria.In the seven data sets,phylogenetic tree constructed by IR region showed a lower relatively resolution,and the phylogenetic trees constructed by the other six data sets have higher support value.Phylogenetic analysis results show that chloroplast genome data can effectively solve the phylogenetic relationships among different subgenera as well as and main branches(or sections)within subgenera,but can not solve the phylogenetic interspecific relationships within secitons,especially among species with rapid radiation evolution.