Chloroplast Genomes Of Ten Primula Species (primulaceae)

Primula is the largest genus in the family Primulaceae with approximately 500 species,where they are distributed mainly throughout temperate and arctic areas of the Northern Hemisphere.The phylogenetic relationships within Primula are not clearly resolved,mainly due to intra-and interspecific morphological variation,which caused by frequent hybridization and introgression.Due to its particular advantages,such as small size,uniparental inheritance,low substitution rates,and high conservation in terms of the gene content and genome structure,the chloroplast genome is considered as a very promising tool for phylogenetic studies.In this study,we sequenced and assembled four complete chloroplast genomes(Androsace laxa,Primula handeliana,Primula woodwardii,and Primula knuthiana)in order to compare the ten Primula species(including seven published chloroplast genomes)by bioinformatics methods and to document the phylogenetic relationships among the Primula taxa.Our study laid the foundation and provided more sequence resources for further phylogenetic studies of the genus Primula.It also provided a basis for clarifying the evolutionary mechanisms of chloroplast genome in this genus.The main contents and results of this study are as follows:1.The chloroplast genome sequence analyses of Androsace laxaThe size of A.laxa chloroplast genome is 151,942 bp with a typical quadripartite structure,including a large single copy region(LSC,83,078 bp),a small single copy region(SSC,16,924 bp),and a pair of inverted repeats(IRs,25,970 bp).This genome contained 132 genes,including 87 protein-coding genes,37 t RNA genes,and eight r RNA genes.Among these genes,15 genes harbored a single intron and three genes harbored two introns.Seven t RNA genes,seven protein-coding genes and all four r RNA genes were completely duplicated in the IR regions.The GC content of A.laxa chloroplast genome is 37.3%,while the corresponding values of the LSC,SSC and IR regions are 35.2,30.9 and 42.7%,respectively.Moreover,A total of 44 repeats and 65 SSRs were identified in the chloroplast genome of A.laxa.2.Comparative chloroplast genome analyses of Primula speciesThe sizes of the cp genomes of the ten Primula species ranged from 150,785 bp to 153,757 bp,where they had a typical quadripartite structure,including an LSC region(82,048-84,479 bp)and an SSC region(17,568-17,896 bp),separated by a pair of IR regions(25,182-25,855 bp).The Primula cp genomes contained 130-132 genes,including 85-86,37 and eigth protein-coding,t RNA and r RNA genes,respectively.The ten Primula cp genomes were similar in terms of their gene content and order,GC content,and codon usage.Synteny analysis revealed no rearrangements in the cp genomes of primula.A total of 26-45 repeats and 36-61 SSRs were identified in the cp genome of primula.The ten Primula cp genomes exhibited moderate sequence divergence.As expected,coding and IR regions exhibited more conserved than non-coding and SC regions,respectively.The ten Primula cp genomes exhibited more obvious differences at the IR/SC boundaries.3.Phylogenetic analyses of the genus PrimulaTo investigate the phylogenetic position of Primula,we used 31 complete cp genomes.76 shared protein-coding genes,codon positions 1 + 2,and codon position 3 were used to conduct the phylogenetic analysis.All trees clearly identified that Primula was monophyletic and more closely related to Androsace than other species in Primulaceae with a high support value.Therefore,A.laxa was used as the outgroup in the phylogenetic analyses of genus Primula.We then constructed six datasets(whole cp genome,protein-coding regions,LSC,SSC,IRs,and introns & intergenic spacers)to analyze the phylogenetic relationships among the members of the genus Primula.The phylogenetic trees,which were based on six datasets,produced two topological structures.Differences mainly included the positions of the clade of P.knuthiana-P.veris.