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.
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| http://dx.doi.org/10.7717/peerj.16272 | DOI Listing |
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