Sequencing and comparative analysis of the chloroplast genome of Ribes odoratum provide insights for marker development and phylogenetics in Ribes

Ribes odoratum, commonly known as clove currant, is a perennial deciduous shrub noted for its long-lasting fragrant flowers and edible fruits. Owing to its ornamental values, this species has been widely used in city gardening and urban landscaping. Here, the complete cp genome of R. odoratum was de novo assembled for the first time. The plastome is 157,152 bp in length, with a GC content of 38.2%. The cp genome featured a typical quadripartite structure, consisting of a pair of inverted repeat regions of 25,961 bp, separated by a large single copy region of 86,896 bp, and a small single copy region of 18,333 bp. A total of 131 genes were annotated in the plastome, including 86 protein coding genes, 37 tRNA genes, and 8 rRNA genes. 56 SSRs were identified, among which, 82.35% were located in the intergenic regions. A strong A/T bias in base composition was observed in these cpSSRs. In addition, 49 repeats of different sizes and types were also found in the plastome. Through comparison, seven divergence hotspots were identified between the cp genomes of R. odoratum and R. fasciculatum var. chinense. Sequences of these divergent regions could be developed as potential markers for species delimitation in further studies. We re-investigated the relationship aomong 32 Saxifragales species through plastome-based phylogenywhich revealed that R. odoratum as a sister of R. fasciculatum var. chinense. Thus, our study provides genomic resources and valuable reference for marker development and phylogenomics in Ribes. Supplementary information The online version of this article (10.1007/s12298-021-00932-4) contains supplementary material, which is available to authorized users.