Chromosome-scale genome, together with transcriptome and metabolome, provides insights into the evolution and anthocyanin biosynthesis of Rubus rosaefolius Sm. (Rosaceae)

Abstract

Rubus rosaefolius is a kind of red raspberry possessing high nutritional and pharmaceutical value. Here we present a chromosome-level draft genome of R. rosaefolius. Of the total 131 assembled scaffolds, 70 with a total size of 219.02 Mb, accounting for 99.33% of the estimated genome size, were anchored to seven pseudochromosomes. We traced a whole-genome duplication (WGD) event shared among members of the Rosaceae family, from which were derived 5090 currently detectable duplicated gene pairs (dgps). Of the WGD-dgps 75.09% underwent purifying selection, and approximately three-quarters of informative WGD-dgps expressed their two paralogs with significant differences. We detected a wide variety of anthocyanins in the berries of R. rosaefolius, and their total concentration remained relatively stable during berry development but increased rapidly during the ripening stage, mainly because of the contributions of pelargonidin-3-O-glucoside and pelargonidin-3-O-(6′′-O-malonyl)glucoside. We identified many structural genes that encode enzymes, such as RrDFR, RrF3H, RrANS, and RrBZ1, and play key roles in anthocyanin biosynthesis. The expression of some of these genes significantly increased or decreased with the accumulation of pelargonidin-3-O-glucoside and pelargonidin-3-O-(6′′-O-malonyl)glucoside. We also identified some transcription factors and specific methylase-encoding genes that may play a role in regulating anthocyanin biosynthesis by targeting structural genes. In conclusion, our findings provide deeper insights into the genomic evolution and molecular mechanisms underlying anthocyanin biosynthesis in berries of R. rosaefolius. This knowledge may significantly contribute to the targeted domestication and breeding of Rubus species.

Acknowledgements

This work was funded by the science and technology plan project of Guizhou Province [(2019) 4318] and [(2021) 239], the science and technology plan project of Guiyang City [2021]3-22, and first-class discipline of Kaili University (Horticulture) [grant number 202102]. We are very grateful to the experimenters and analysts at Biomarker Inc. (www.biomarker.com.cn) who took part in this study.

Author contributions

Y.S.W. and Q.Y.Z. designed the experiments, J.Y.G. and Q.Y.Z. collected samples and took part in conducting experiments, Y.S.W. and Q.Y.Z. took part in analyzing the data, and Y.S.W. wrote the paper.

Data availability statement

The draft genome sequence was deposited in the China National Center for Bioinformation Database (https://bigd.big.ac.cn/gsub/, accession number CRA011290). The clean raw data of the long-read and short-read transcriptomes of young stems, young roots, young leaves, calyxes, petals, stamens, young berries, coloring berries, and mature berries were also deposited in the China National Center for Bioinformation Database (https://bigd.big.ac.cn/gsub/, accession numbers CRA011285 and CRA012463).

Conflict of interest

The authors declare no conflicts of interest.

Supplementary data

Supplementary data are available at Horticulture Research online.

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