Chloroplast Genome Characteristics And Phylogeny Of The Genus Rosa

The genus Rosa,belonging to the Rosaceae family,is divided into 2 subgenera,7series and 9 sections.This genus,including ca.200 species,distribute in Asia,Europe,Africa and North America.There are ca.95 species distribute in China.Up to now,the studies on Rosa mainly focus on chemical composition,cultivations,breeding and food developments etc..There is still lack of comprehensive taxonomic studies especially molecular phylogeny of the genus Rosa,even though some whole chloroplast genomes or whole genomes reported.Due to the fact that interspecies can easily produce fertile offspring through hybridization,there are a large number of hybrids in the genus Rosa.It also increases the difficulty of classification for species of the genus Rosa.In addition,some sections of the genus Rosa,such as Sect.Chinenses DC.,and Sect.Rosa,there are a large number of artificially cultivated hybrids or natural hybrids.Due to insufficient studies on interspecific hybridization,there has been controversy on the interspecific relationships,phylogenetic relationships,and ancestral origins of some species in the genus Rosa.In recent years,the whole chloroplast genomes have been widely used in species identification and phylogenetic analysis.In this study,the whole chloroplast genomes of 68 individuals of the genus Rosa were obtained through next-generation sequencing.The sequencing,annotation,comparative genomics analysis and phylogenetic analysis were conducted,and the following results were obtained:The chloroplast genomes of the Rosa exhibited a typical quadripartite structure.The genome length is between 156,291-157,327 bp.The length of LSC,SSC,and IR are 85,408-86,515 bp,18,653-19,008 bp,51,898-52,158 bp,respectively.The GC content of the whole chloroplast genome,LSC,SSC,and IR region is 37.2-37.3%,35.1-35.3%,31-31.4%,42.7-42.8%,respectively.A total of 2,022 long repeat sequences of 4 types are detected,and the number,proportion and distribution of each repeat sequence in each individual were analyzed.In addition,a total of 5,593 simple sequence repeats(SSRs)loci were detected in the 68 individuals of Rosa.Through the relative synonymous codon usage analyses of the chloroplast genome,the number of codon is found to be between 52,097-52,442.The relative synonymous codon usage(RSCU)value of 32 codons is greater than 1,indicating a strong preference,while the RSCU value of 29 is less than 1,indicating a weak preference.The stop codon UAA has the most occurrence when compares to stop codons UAG and UGA.All the preferred codons end with the amino acid A or U.The results of the m VISTA and nucleotide polymorphism analysis of the Rosa show that the 68 chloroplast sequences of Rosa contain certain variations.In general,the IR is more conservative than the LSC and the SSC regions,and the variations mainly occur in the non-coding region.The collinearity analysis shows that the chloroplast DNA of the Rosa is highly collinear,and there is no rearrangement or inversion of large gene segments observed.The IR boundary analysis of the Rosa shows that there is no contraction/expansion of the IR region in Rosa,and the genes presented adjacent to the boundary were identical.Phylogenetic trees of the genus Rosa were constructed based on the whole chloroplast genomes.The results exhibited that: The genus Rosa is a monophyletic group in Rosaceae.Species of the Sect.Carolinae should be transferred to Sect.Cinnamomeae.The species,R.centifolia and R.’Portland rose’,should be transferred into Sect.Canina.The topology of molecular phylogenetic trees mismatch the conventional subdivision of the genus Rosa mainly based on morphological characters.We propose more individuals should be included in future,as insufficient taxa of this study.The whole genome would be helpful to solve the phylogeny of Rosa,as more phylogenetic information can be obtained.