High-quality genome of black wolfberry (Lycium ruthenicum Murr.) provides insights into the genetics of anthocyanin biosynthesis regulation

Abstract

Black wolfberry (Lycium ruthenicum Murr.) is an important plant for ecological preservation. In addition, its fruits are rich in anthocyanins and have important edible and medicinal value. However, a high-quality chromosome-level genome for this species is not yet available, and the regulatory mechanisms involved in the biosynthesis of anthocyanins are unclear. In this study, haploid material was used to assemble a high-quality chromosome-level reference genome of Lycium ruthenicum, resulting in a genome size of 2272 Mb with contig N50 of 92.64 Mb, and 38 993 annotated gene models. In addition, the evolution of this genome and large-scale variations compared with the Ningxia wolfberry Lycium barbarum were determined. Importantly, homology annotation identified 86 genes involved in the regulatory pathway of anthocyanin biosynthesis, five of which [LrCHS1 (evm.TU.Chr05.295), LrCHS2 (evm.TU.Chr09.488), LrAOMT (evm.TU.Chr09.809), LrF3’5’H (evm.TU.Chr06.177), and LrAN2.1 (evm.TU.Chr05.2618)] were screened by differential expression analysis and correlation analysis using a combination of transcriptome and metabolome testing. Overexpression of these genes could significantly up- or downregulate anthocyanin-related metabolites. These results will help accelerate the functional genomic research of L. ruthenicum, and the elucidation of the genes involved in anthocyanin synthesis will be beneficial for breeding new varieties and further exploring its ecological conservation potential.

Acknowledgements

This work was sponsored by the Key Research & Development Program of Ningxia Hui Autonomous Region (2022BBF01001 and 2021BEF02002), the National Natural Science Foundation of China (U23A20221), and the Innovative Research Group Project of Ningxia Hui Autonomous Region (No. 2021AAC01001).

Author contributions

J.Z., Y.X., and A.X. conceived and designed the research. Q.L. and H.L. prepared the materials. T.S., Y.C., S.G., W.T., W.A., J.Z., and Y.Y. performed sampling, sequencing, genome assembly, and transcriptome analyses. J.H., R.Z., X.L., Y.W., X.Z., Z.S., L.D., X.Q. B.Z., R.W., Y.L., T.H., H.L., and S.S. contributed to the project discussion. Y.X., H.L., and J.Z. wrote the manuscript. J.Z., Y.C., A.X., and Y.X. revised the manuscript. All authors read and approved the final manuscript.

Data availability

Data supporting the findings of this work are available within the paper and the Supplementary Tables and Figures. The genome assembly, HiFi reads and HiC data have been deposited into the National Center for Biotechnology Information Sequence Read Archive database with accession numbers JAUDPO000000000, PRJNA1099465 and PRJNA1099464, respectively. The genome assembly data is also available on the Figshare platform (https://doi.org/10.6084/m9.figshare.26550406).

Conflict of interest statement

All the authors declare that there is no conflict of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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