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Article|23 Oct 2024|OPEN
High-quality genome of black wolfberry (Lycium ruthenicum Murr.) provides insights into the genetics of anthocyanin biosynthesis regulation
Yuhui Xu1,8 , Haoxia Li2,8 , Tongwei Shi3,8 , Qing Luo1 , Yuchao Chen4 , Shenghu Guo4 , Weiwei Tian5 , Wei An1 , Jian Zhao1 , Yue Yin1 , Jun He1 , Rui Zheng6 , Xiaojie Liang1 , Yajun Wang1 , Xiyan Zhang1 , Zhigang Shi1 , Linyuan Duan1 , Xiaoya Qin1 , Ting Huang1 , Bo Zhang1 , Ru Wan1 , Yanlong Li1 , Youlong Cao1 and Hui Liu7 , Sheng Shu7 , Aisheng Xiong7 , , Jianhua Zhao,1 ,
1National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
2Institute of Forestry and Grassland Ecology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
3Planttech technologies Co. Ltd., Beijing, China
4Agricultural Biotechnology Centre, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
5Sichuan Academy of Chinese Medical Sciences, Chengdu 610041, China
6Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China; College of Life Science, Ningxia University, Yinchuan 750021, China
7State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
8These authors contributed equally: Y.X., H.L., and T.S.
*Corresponding author. E-mail: xiongaisheng@njau.edu.cn,zhaojianhua0943@163.com

Horticulture Research 12,
Article number: uhae298 (2025)
doi: https://doi.org/10.1093/hr/uhae298
Views: 1683

Received: 08 Mar 2024
Accepted: 11 Oct 2024
Published online: 23 Oct 2024

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.