Unlocking the genome of black wolfberry: Secrets of anthocyanin biosynthesis
image: Expression patterns of anthocyanin biosynthesis pathway genes and TFs.
Credit: Horticulture Research
Black wolfberry (Lycium ruthenicum), a plant prized for its resilience and high anthocyanin content, has long intrigued scientists seeking to understand its health benefits and adaptive strength. Researchers have now generated a high-quality chromosome-level genome that sheds light on the genetic mechanisms regulating anthocyanin biosynthesis. Through a combination of genome sequencing, comparative genomics, transcriptomics, and metabolomics, the team identified key structural genes and transcription factors responsible for pigment accumulation in the fruit. Functional validation confirmed their regulatory roles, offering new opportunities for breeding wolfberry varieties with enhanced nutritional and medicinal properties while advancing knowledge of how plants adapt to harsh desert environments.
Black wolfberry is native to saline–alkali deserts of northwest China, where it acts as a pioneer species for ecological restoration and provides fruits exceptionally rich in anthocyanins. These pigments, more concentrated in black wolfberry than in blueberries or blackcurrants, contribute antioxidant, anticancer, and anti-aging properties. Yet, despite its ecological and nutritional importance, the absence of a high-quality reference genome has hindered systematic investigation of the plant's biosynthetic and regulatory networks. Current insights into anthocyanin pathways, derived mainly from related species, remain incomplete. Due to these challenges, it is necessary to conduct in-depth research on black wolfberry to fully clarify its genetic basis of pigment production and adaptation.
A research team from the Ningxia Academy of Agriculture and Forestry Sciences, Nanjing Agricultural University, and collaborating institutes published (DOI: 10.1093/hr/uhae298) their findings on February 1, 2025, in Horticulture Research. By assembling a 2.27-Gb genome of black wolfberry using PacBio HiFi and Hi-C technologies, the team achieved an unprecedented resolution of its genetic landscape. They identified critical structural genes such as LrCHS1, LrCHS2, LrAOMT, LrF3'5'H, and transcription factor LrAN2.1, which regulate anthocyanin biosynthesis, and experimentally validated their functions in pigment accumulation.
The researchers used haploid material to overcome the challenges of high heterozygosity and produced a chromosome-level genome with a contig N50 of 92.64 Mb, representing a significant improvement over earlier draft assemblies. Comparative analysis revealed whole-genome duplication events, expansions of stress-related gene families, and divergence from the closely related Lycium barbarum around 7.4 million years ago. Multiomics integration identified 86 genes involved in anthocyanin pathways, with LrCHS1, LrCHS2, LrAOMT, LrF3'5'H, and LrAN2.1 emerging as key regulators. Functional tests through transient transformation demonstrated their distinct roles in modulating pigment metabolites, with some genes promoting accumulation of cyanidin and delphinidin derivatives, while LrAN2.1 acted as a negative regulator for specific compounds. These findings not only explain why black wolfberry contains uniquely high levels of anthocyanins but also illustrate how gene interactions and feedback mechanisms fine-tune pigment synthesis during fruit development. Moreover, genome differentiation analyses highlighted structural variations between black and red wolfberries that may underlie differences in anthocyanin content and ecological adaptation.
“Our work delivers the first high-quality genome of black wolfberry, a plant both nutritionally valuable and ecologically vital,” said Prof. Jianhua Zhao, senior author of the study. “By pinpointing the genes responsible for anthocyanin biosynthesis, we can now better understand how these health-promoting pigments are produced and regulated. This genomic foundation paves the way for precision breeding strategies that enhance fruit quality, resilience, and medicinal applications, while also offering a resource for studying plant adaptation to extreme desert environments.”
The new genome resource opens multiple avenues for science and agriculture. For breeders, the identified structural genes and transcription factors provide direct targets for developing wolfberry cultivars with improved anthocyanin content and stress resistance. For human health, understanding the genetic regulation of these compounds may lead to new functional foods or nutraceuticals with antioxidant and protective benefits. From an ecological perspective, insights into stress-adaptation genes could support restoration of saline–alkali soils and arid landscapes. Overall, the study highlights the potential of integrating genomic resources with molecular breeding to harness black wolfberry's dual value as a health food and an environmental protector.
###
References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae298
Funding information
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).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.