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

The complete chloroplast genomes of red currant cultivar 'Belaya Potapenko' and gooseberry cultivar 'Nekrasovskij' were sequenced and assembled for the first time. The plastomes are 157,802 bp and 157,559 bp in length for Ribes rubrum and R. uva-crispa, respectively. The R. rubrum cp genome is 243 b.p. longer. It has one more protein-coding gene ycf1, which is pseudogenized in the R. uva-crispa cp genome. In total, 56 and 54 simple sequence repeats (SSRs) were identified within the assembled plastid genomes. The SSR content of plastid genomes was assessed for the 18 Saxifragales species. Phylogeny inference based on plastome data of 18 Saxifragales revealed that all Ribes species are clustered together on the phylogenetic tree, though R. fasciculatum seems to be the most distant from the other analyzed Ribes species. The position of taxa inside the Ribes genus clade does not support the concept of its division into five subgenera. All Ribes species share approximately the same set of protein-coding genes in their plastome sequences. There was multiple independent pseudogenization of the ycf1 gene within the Ribes genus as well as other Saxifragales taxa. Negative selection was observed for most of the genes in both the Ribes group and Saxifragales. A positive selection ratio was observed only inside the Ribes group for the ycf4 and clpP genes. Together with positive selection signatures, pseudogenization events of ycfs genes perhaps reflect that these genes' evolution was important for Ribes' adaptation. Thus, our study provides genomic resources and valuable reference for marker development, and makes some clarifications of the phylogenomics of the Ribes genus.

Automated summary

The complete chloroplast genomes of red currant and gooseberry cultivars were sequenced and assembled, revealing differences in genome length and protein-coding genes. Phylogenetic analysis showed that Ribes species clustered together, with Ribes fasciculatum being the most distant. All Ribes species share a similar set of protein-coding genes in their plastome sequences. Negative selection was observed for most genes in both the Ribes group and Saxifragales, while positive selection was observed for ycf4 and clpP genes in the Ribes group. Pseudogenization events of ycf genes may reflect their importance in Ribes' adaptation. The study provides valuable genomic resources and clarifications for marker development and phylogenomics of the Ribes genus.