Chloroplast Genomes Of Sibbaldianthe Species In China

Sibbaldianthe Juz.is a genus of family Rosaceae Juss.,subfamily Rosoideae(Juss.)Arn.,tribe Potentilleae Sweet.Seven species are distributed in Eurasia in the world.All seven species occur in China.This genus has some economic value.So far,there has not been any research on Sibbaldianthe from the perspective of chloroplast genome.High-throughput sequencing and bioinformatics methods were used to sequence,assemble,and annotate the whole chloroplast genomes of four species(Sibbaldianthe adpressa,S.bifurca,S.moorcroftii,S.sericea)and 12 populations of Sibbaldianthe.Comparative study of the whole chloroplast genomes of Sibbaldianthe was carried out,and the molecular markers was developed using the whole chloroplast genome data,and the systematic position of Sibbaldianthe in Potentilleae and the phylogenetic relationships among the Sibbaldianthe species were also inferred.The whole chloroplast genome sequences obtained in this study provide “Ultra-barcoding” for the identification of Sibbaldianthe species;the developed molecular markers will presumably be very useful for the identification of Sibbaldianthe species,and the development of species population genetics research and phylogeny study.This study can provide basic data for the classification and phylogeny study of Sibbaldianthe and lay a foundation for further research.The main contents and results of this study are as follows:1.In this study,the complete chloroplast genomes of four species and 12 populations of Sibbaldianthe were obtained.Like most angiosperm chloroplast genomes,the chloroplast genomes of Sibbaldianthe species present a typical quadripartite structure: a large single copy region(LSC),a small single copy region(SSC)and two inverted repeats(IRs).In terms of genome size,gene content and gene order,the chloroplast genome of Sibbaldianthe is highly conserved.The total length of the chloroplast genome sequence of Sibbaldianthe is 154,610bp-155,105bp;the length of the LSC is84,536bp-84,823 bp,and the length of the SSC is 17,846bp-18,272 bp,and the length of the IR is 26,028bp-26,058 bp.The total GC content of the genome is 37.2%;the GC content of the LSC is 35.0%-35.1%;the GC content of the SSC is 31.0%-31.4%;the GC content of the IR is 42.8%.The chloroplast genomes of Sibbaldianthe encode 129 genes,including 84protein-coding genes(CDS),8 ribosomal RNA genes(r RNA)and 37 transfer RNA genes(t RNA).The IR/SC boundary analysis showed that the relative position of genes near the boundary has slight changes,and there is basically no obvious contraction and expansion in the IR zone.The synteny analyses showed that there was no inversion and gene rearrangement in the chloroplast genomes of Sibbaldianthe.2.A total of 264 exons,introns and intergenic spacer(IGS)fragments of the 12 chloroplast genome sequences of Sibbaldianthe were analysed and 13 gene fragments(rpl32-trn L-UAG,trn G-GCC-trnf M-CAU,trn H-GUG-psb A,rps2-rpo C2,trn R-UCU-atp A,rps15-ycf1,psa J-rpl33,ndh F-rpl32,trn G-UCC-trn R-UCU,atp F-atp H,rps16 intron,5'-rps12-clp P,5'-trn K-UUU-rps16)were chosen as candidate molecular markers for Sibbaldianthe.These candidate molecular markers can play an important role in species identification,population genetics research and phylogeny research.3.Based on the chloroplast genome sequences,Bayesian inference(BI)and Maximum likelihood(ML)methods were used to construct phylogenetic trees for Sibbaldianthe and related species.The topologies of the phylogenetic trees constructed by the two methods is completely consistency.The results of phylogenetic analysis strongly support the monophyly of tribe Potentilleae,and Sibbaldianthe belongs to subtribe Fragariinae and is closely related to Sibbaldia,Alchemila and Farinopsis.The results also support the separation of Sibbaldia adpressa and Sibbaldia sericea from Sibbaldia into Sibbaldianthe,and the separation of Potentilla bifurca and Potentilla moorcoftii from the Potentilla into Sibbaldianthe.