Structural characteristics and phylogenetic evolution of chloroplast genomes in Rubus genus
[Objective]The study provides a basis for the classification and evolution of Rubus,which provides theoretical support for DNA barcoding and protection of Rubus species.[Method]Using bioinformatics and comparative genomics methods to analyze the chloroplast genome size,structure,composition,repeats,boundary extension,genomic collinearity,forward selection and phylogeny of 16 Rubus.[Result]The chloroplast genome of 16 plants had a typical tetrad structure,length of 155 286 bp to 156 668 bp,37.15%of average GC content.The variation of genome size was small and the length of SSC region and IR region was more stable.In the functional classification of coding genes,it was found that only eight Rubus species had two full copies of ycf1 gene and some genes had only a single copy in some plats.The results of boundary expansion analysis showed that there was no obvious contraction or expansion in the boundary of the reverse repetition region.The results of collinearity and phylogenetic analysis showed that there was a high similarity between R.pacificus and the other 15 plants.R.pacificus and R.pyrifolius var.Permollis,R.bambusarum were close relatives,but had the lowest similarity with R.bambusarum.The Taijima'test analysis showed that there was a tendency of population expansion in Rubus,and protein-coding genes had a certain degree of purification selection or neutral selection.[Conclusion]The chloroplast genome of Rubus is highly conserved,the closer the relationship between species,the higher the chloroplast genome similarity,but the reverse is not true.Based on the sequence of chloroplast genomes,we can locate them in the phylogenetic tree and analyze their relationship.
NETL
NSTL
万方数据
