Organellar genome evolution in Ribes L.: hotspots of mutation, sequence transfer, codon usage, and phylogenetic context

Abstract

Ribes genus from the Grossulariaceae family, have been used in the food industry and for medicinal purposes for years. Despite the valuable medicinal values and the widespread occurrence of Ribes, many species remain understudied. One of these is the alpine currant Ribes alpinum L., which occurs natively in Europe. The study aimed to thoroughly understand and characterize the organelle genomes of R. alpinum, conduct their comparative analysis with available data for other representatives of Grossulariaceae and, in the case of the chloroplast genome, also with Saxifraga insolens Irmsch., a representative of the closely related Saxifragaceae family. The analysis of plastome interspecific variation revealed several hotspots of variation which could be useful as potential phylogenetic markers or specific DNA barcodes. The phenomenon of sequence transfer between the chloroplast and mitochondrial genomes and the relative synonymous codon usage between the plastome and mitogenome were also analyzed. A phylogenetic inference based on the chloroplast genome sequence questioned earlier reports of a close relationship of R. alpinum to R. rubrum and confirmed its affiliation with an early-diverged phylogenetic line together with R. fasciculatum. Analysis of hotspots of variation in chloroplast genome allowed us to indicate petN-psbM and trnS-trnG as high-utility barcode sequences, competitive with standard barcodes and the ycf1 gene.