T2T gap-free genome assembly and genomic features of Scutellaria baicalensis. A Image of the S. baicalensis plant. B Visualization of gene density and the distribution of centromeress and telomere in the S. baicalensis genome. The scale represents chromosomes in a 500 kb window. C Landscape of the S. baicalensis genome assembly. The circles (outer to inner) represent: pseudochromosomes (Chr1 to Chr9), gene density, repetitive sequences density, GC content, and duplicated gene links (3934 gene pairs in total) within the genome. Chromosomes are shown in a 50 kb window.
Scutellaria baicalensis, widely used in traditional Chinese medicine for its anti-inflammatory and antiviral effects, has been difficult to study due to incomplete genome data. Previous attempts at genome assembly left significant gaps, limiting the understanding of key biosynthetic pathways for flavonoids, which contribute to both its health benefits and flower pigmentation. Addressing these limitations, a comprehensive genome assembly was required to better understand the plant’s genetic architecture.
Scientists at the Shanghai Key Laboratory of Plant Functional Genomics led the research, with findings (DOI: 10.1093/hr/uhad235) published in Horticulture Research on November 17, 2023. Using advanced sequencing technologies including Pacbio HiFi, Nanopore ultra-long reads, and Hi-C, the team achieved the first telomere-to-telomere (T2T) genome assembly for S. baicalensis, covering 384.59 Mb and organized into nine pseudochromosomes. The study identified key genes within the CYP450 gene family responsible for flavonoid hydroxylation, crucial for anthocyanin biosynthesis and the plant’s vibrant blue-purple flowers.
This research represents a major step forward in genomic studies of S. baicalensis, particularly in understanding anthocyanin biosynthesis. The newly assembled T2T genome enables more detailed analysis of the CYP450 family, revealing three genes (SbFBH1, 2, 5) responsible for flavonoid 3’-hydroxylation and one gene (SbFBH7) for flavonoid 3’,5’-hydroxylation. These genes regulate the production of cyanidin and delphinidin, the pigments that generate the plant's blue and purple hues. Beyond flower pigmentation, this complete genome provides a foundation for targeted metabolic engineering and further research into the plant’s well-documented anti-inflammatory and antiviral properties.
Dr. Qing Zhao, lead researcher at the Shanghai Key Laboratory of Plant Functional Genomics, stated: “Our gap-free genome assembly of S. baicalensis marks a significant achievement in medicinal plant genomics. By decoding the full genetic sequence, we’ve identified crucial genes involved in anthocyanin biosynthesis. This not only enhances our understanding of flower coloration but also paves the way for improving the plant’s health benefits. It’s a key step toward future innovations in both medicinal and ornamental plant development.”
The potential applications of this research are substantial, particularly for horticulture and pharmaceuticals. The newly identified genes involved in flavonoid biosynthesis could be harnessed to engineer S. baicalensis and other plants for specific traits such as enhanced flower colors or increased production of medicinal compounds. Moreover, the gap-free genome will serve as a critical resource for scientists exploring flavonoid and anthocyanin pathways, with implications for developing stronger anti-inflammatory and antiviral therapies from this widely used medicinal herb.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhad235
Funding information
This work is sponsored by Natural Science Foundation of Shanghai (22ZR1479500), Special Fund for Scientific Research of Shanghai Landscaping & City Appearance Administrative Bureau (G212401), Ministry of Science and Technology of China (YDZX20223100001003), Funding for Shanghai science and technology promoting agriculture from Shanghai Agriculture and Rural Affairs Commission (Hu Nong Ke Chan Zi (2023) No. 8) and Youth Innovation Promotion Association of Chinese Academy of Sciences. Q.Z. is also supported by the Shanghai Youth Talent Support Program and SANOFI-SIBS scholarship.
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, 2022. 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.
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