Complete chloroplast genome assembly and phylogenetic analysis of blackcurrant (Ribes nigrum), red and white currant (Ribes rubrum), and gooseberry (Ribes uva-crispa) provide new insights into the phylogeny of Grossulariaceae
Xinyu Sun,
Ying Zhan,
Songlin Li,
Yu Liu,
Qiang Fu,
Xin Quan,
Jinyu Xiong,
Huixin Gang,
Lijun Zhang,
Huijuan Qi,
Aoxue Wang,
Junwei Huo,
Dong Qin,
Chenqiao Zhu
Affiliations
Xinyu Sun
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Ying Zhan
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Songlin Li
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Yu Liu
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Qiang Fu
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Xin Quan
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Jinyu Xiong
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Huixin Gang
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Lijun Zhang
National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
Huijuan Qi
National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, National Development and Reform Commission, Harbin, Heilongjiang, China
Aoxue Wang
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Junwei Huo
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Dong Qin
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Chenqiao Zhu
College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
Background Blackcurrant (Ribes nigrum), red currant (R. rubrum), white currant (R. rubrum), and gooseberry (R. uva-crispa) 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 Ribes 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 Ribes 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 Ribes cp genomes. Red currant and white currant have 100% identical cp genomes partially supporting the hypothesis that white currant (R. rubrum) is a fruit color variant of red currant (R. rubrum). The most polymorphic genic and intergenic region is ycf1 and trnT-psbD, respectively. The phylogenetic analysis demonstrated the monophyly of Grossulariaceae in Saxifragales and the paraphyletic relationship between Saxifragaceae and Grossulariaceae. Notably, the Grossularia subgenus is well nested within the Ribes subgenus and shows a paraphyletic relationship with the co-ancestor of Calobotrya and Coreosma sections, which challenges the dichotomous subclassification of the Ribes genus based on morphology (subgenus Ribes and subgenus Grossularia). These data, results, and insights lay a foundation for the phylogenetic research and breeding of Ribes species.
