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Article|17 Nov 2023|OPEN
Gap-free genome assembly and CYP450 gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis 
Tianlin Pei1,2 ,† , Sanming Zhu1,3 ,† , Weizhi Liao1,4 , Yumin Fang1 , Jie Liu1 and Yu Kong1 , Mengxiao Yan1 , Mengying Cui1 , , Qing Zhao,1,2 ,
1Shanghai Key Laboratory of Plant Functional Genomics and Resources, CAS Center for Excellence in Molecular Plant Sciences Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
2State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
3National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, 271018, China
4Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
*Corresponding author. E-mail:,
Both authors contributed equally to the study.

Horticulture Research 11,
Article number: uhad235 (2024)
Views: 53

Received: 14 Aug 2023
Accepted: 01 Nov 2023
Published online: 17 Nov 2023


Scutellaria baicalensis Georgi, a member of the Lamiaceae family, is a widely utilized medicinal plant. The flavones extracted from S. baicalensis contribute to numerous health benefits, including anti-inflammatory, antiviral, and anti-tumor activities. However, the incomplete genome assembly hinders biological studies on S. baicalensis. This study presents the first telomere-to-telomere (T2T) gap-free genome assembly of S. baicalensis through the integration of Pacbio HiFi, Nanopore ultra-long and Hi-C technologies. A total of 384.59 Mb of genome size with a contig N50 of 42.44 Mb was obtained, and all sequences were anchored into nine pseudochromosomes without any gap or mismatch. In addition, we analysed the major cyanidin- and delphinidin-based anthocyanins involved in the determination of blue-purple flower using a widely-targeted metabolome approach. Based on the genome-wide identification of Cytochrome P450 (CYP450) gene family, three genes (SbFBH12, and 5) encoding flavonoid 3′-hydroxylases (F3′Hs) and one gene (SbFBH7) encoding flavonoid 3′5′-hydroxylase (F3′5′H) were found to hydroxylate the B-ring of flavonoids. Our studies enrich the genomic information available for the Lamiaceae family and provide a toolkit for discovering CYP450 genes involved in the flavonoid decoration.