Gap-free genome assembly and CYP450 gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis

Abstract

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 (SbFBH1, 2, 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.

Acknowledgements

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. We greatly appreciate the experimental facilities and services provided by the office of Chenshan Plant Science Research Center. We also thank Yanbo Huang from Shanghai National Forest Germplasm Resource Center of Lamiaceae Plant for the photograph of S. baicalensis in Fig. 1.

Author contributions

The program was initiated and coordinated by T.P. and Q.Z. T.P. and W.L. conducted the analysis of the sequencing data. S.Z. was responsible for gene isolation and enzyme characterization. Y.K. provided assistance with the LC-MS analysis. All authors participated in the data analysis and interpretation. The manuscript was written by T.P. and Q.Z. and was reviewed and approved by all authors.

Data availability

Illumina RNA sequencing data of different tissues from S. baicalensis are extracted from the Sequence Read Archive (SRA) database (www.ncbi.nlm.nih.gov/sra) with the accession number SRP156996. The two previous versions of S. baicalensis genome are available in the National Genomics Data Center (NGDC, https:// bigd.big.ac.cn/gwh) with accession number GWHAOTC00000000 and GWHAOTO00000000, respectively. The T2T gap-free genome assembly of S. baicalensis is available in NGDC with accession number GWHDEDD00000000.

Conflict of interest statement

The authors declare no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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