| The genus Ribes L.has gradually received attention and research at home and abroad for its nutritional benefits,high economic value and wide distribution,but the development and utilization of Ribes is still in its early stage,and the taxonomic analysis of Ribes within the genus has not yet reached a more authoritative conclusion abroad.In this study,the chloroplast genomes of four species of Ribes were subjected to whole-genome high-throughput sequencing,chloroplast genome assembly,SSR loci and structural repeat sequence analysis,SNP and In Del loci,nucleotide polymorphism(Pi)analysis with those of Ribes published in NCBI,and phylogenetic trees of chloroplast genomes were constructed to clarify the interspecific relationships of nine interspecific relationships among plants of the genus Ribes.The genetic distances of blackcurrant,red currant,white currant and gooseberry were determined by cp SSRs and n SSRs,and the evolutionary tree obtained from the chloroplast genome was verified.The conclusions are as follows.(1)All four chloroplast genomes contain complete ring-mounted tetrameric structures with full sequence lengths in the range of 157,450 bp(R.nigrum)-157,802 bp(R.rubrum).The total GC content of the genome was 38.08 %(R.rubrum)-38.21 %(R.uva-crispa).The four genomes were annotated with 131 genes,including 86 protein-encoding genes,8 rRNA genes,and 35 tRNA genes.21 genes contained one intron,and two genes contained two introns.(2)A total of 51(R.rubrum)-64(R.uva-crispa)structural repeats were sieved from the chloroplast genomes of the four Ribes materials,with the most tandem repeats.A total of 40-54 SSR loci were screened,which were composed of both single-base repeats and double-base repeats,and no double-base repeats were present in blackcurrant.The cpSSR loci is mainly present in the large single copy(LSC),which mainly present in the intergenic spacer(IGS).This molecular marker development provided the basic data for subsequent marker development work.(3)Comparison of contraction and expansion of the inverted repeat regions(IR)boundary region of nine Ribes plants revealed that genes or IGS regions in the IR boundary regions showed high polymorphism.SNP and In Del loci were identified for the nine Ribes genus sequences,and a total of 3,322 SNP loci and 485 In Del loci were found.Visualization of the highly variable loci showed that the nucleotide diversity(Pi)of the nine plasmids showed variation in the range of 0 to 0.21.The IGS regions with polymorphisms greater than 0.019 were trn T-psb D,psb Z-trn G,ndh Frpl32,rpl32-trn L,and ccs A-ndh D.The ycf1 gene contained three intervals with polymorphisms greater than 0.019.(4)The ML tree results confirmed the viewpoint that plants in the Grossulariaceae family are independent of those in the Saxifragaceae family,and the Grossulariaceae family is divided into four branches.In addition,by analyzing the chloroplast genomes of the red and white currant,it was found that the sequence information obtained was completely consistent.Based on this,it was determined that these two species may have a common ancestor,and their relationship is very close,supporting the view that the white currant is a variant of the red currant.In order to distinguish the two species in breeding,it is suggested that the Latin name of white currant should be changed to Ribes rubrum var.alba.(5)Five pairs of cpSSR primers were screened from the chloroplast genome,and 26 pairs of n SSR primers were screened from the transcriptome data.Through the phylogenetic analysis of 94 species of Ribes plants,it was found that using cp SSR primers and n SSR primers could apply them to population structure analysis,genetic relationship identification,and ultimately to protect core germplasm resources. |
PDF Full Text Request