Complete chloroplast genome assembly and phylogenetic analysis of blackcurrant (), red and white currant (), and gooseberry () provide new insights into the phylogeny of Grossulariaceae.

BACKGROUND

Blackcurrant (), red currant (), white currant (), and gooseberry () belong to Grossulariaceae and are popular small-berry crops worldwide. The lack of genomic data has severely limited their systematic classification and molecular breeding.

METHODS

The complete chloroplast (cp) genomes of these four taxa were assembled for the first time using MGI-DNBSEQ reads, and their genome structures, repeat elements and protein-coding genes were annotated. By genomic comparison of the present four and previous released five cp genomes, the genomic variations were identified. By phylogenetic analysis based on maximum-likelihood and Bayesian methods, the phylogeny of Grossulariaceae and the infrageneric relationships of the were revealed.

RESULTS

The four cp genomes have lengths ranging from 157,450 to 157,802 bp and 131 shared genes. A total of 3,322 SNPs and 485 Indels were identified from the nine released cp genomes. Red currant and white currant have 100% identical cp genomes partially supporting the hypothesis that white currant () is a fruit color variant of red currant (). The most polymorphic genic and intergenic region is and , respectively. The phylogenetic analysis demonstrated the monophyly of Grossulariaceae in Saxifragales and the paraphyletic relationship between Saxifragaceae and Grossulariaceae. Notably, the subgenus is well nested within the subgenus and shows a paraphyletic relationship with the co-ancestor of and sections, which challenges the dichotomous subclassification of the genus based on morphology (subgenus and subgenus ). These data, results, and insights lay a foundation for the phylogenetic research and breeding of species.