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

Abstract

Ribes odoratum, commonly known as clove currant, is a perennial deciduous shrub noted for its longlasting 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.

Plastome Data of Red Currant and Gooseberry Reveal Potential Taxonomical Issues within the Ribes Genus (Grossulariaceae)

“…Ribes is the single genus of the Grossulariaceae family clustered together with representatives of Iteaceae and Saxifragaceae, with the latter being the closest one. The obtained results of phylogeny inference within the order Saxifragales confirm previous phylogenetic studies [54][55][56].…”

“…The size and structure showed high conservation across the plastomes of the 8 Ribes species, implying a close phylogenetic relationship between them. The non-coding regions were more divergent than the protein-coding regions, and this is consistent with comparative analyses in other angiosperms [53,54].…”

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

“…The reference I. tectorum genome (153,253 bp) was the third in size. The coding regions had less divergence than the noncoding sequence regions owing to the variable regions [ 92 – 94 ]. The IR regions were more conserved, whereas the LSC and SSC regions were more divergent.…”