Whole genome and transcriptome reveal flavone accumulation in Scutellaria baicalensis roots

Abstract

Scutellaria baicalensis Georgi is a medicinal plant in the Lamiaceae family that contains high levels of 4’-deoxyflavone and other flavonoids in its roots. Therefore, it has strong potential as a plant resource for researching the biosynthesis of specific flavonoids. In this study, we report on a chromosome-level S. baicalensis genome assembled to nine chromosomes (376.81M) using PacBio, HiSeq XTen, and Hi-C assisted assembly. The assembly ratio was 99.22%, the contig N50 was 1.80 million bases, and the scaffold N50 was 40.57 million bases, with 31896 genes being annotated. Comparative genome analysis revealed that S. baicalensis and Salvia miltiorrhiza belonged to the same branch, and diverged 36.3 million years ago. Other typically correlated species were Boea hygrometrica and Sesamum indicum. We investigated the structural genes involved in flavonoid synthesis in combination with transcriptome sequencing analysis for different tissues (roots, stems, flowers, leaves) of purple, pink, and white flowers. The results revealed that S.baiF6H is involved in the accumulation of baicalein and was significantly increased in both purple roots vs. pink roots and white roots vs. pink roots. S.baiMYB gene family expression pattern analysis and co-expression network analysis revealed that S.baiMYB transcription factors primarily regulated the production of flavonoids in S. baicalensis. S.baiMYB serves as a major factor regulating flavonoid synthesis in the roots, where yeast one-hybrid assays revealed that these transcription factors could bind to the promoter regions of structural genes to control the accumulation of flavonoids. Genome and transcriptome sequencing, co-expression analysis, and yeast one-hybrid experiments provided valuable genetic resources for understanding flavonoid biosynthesis in S. baicalensis. These findings contribute to a better understanding of the accumulation of metabolites in Lamiaceae.

Multi-omics landscape to decrypt the distinct flavonoid biosynthesis of Scutellaria baicalensis across multiple tissues

“…The genome of S. baicalensis was downloaded from the China National Center For Bioinformation ( https://www.cncb.ac.cn/?lang=en ) with accession number GWHBJEC00000000 under BioProject PRJCA009554 [ 31 ]. Depending on the genome of S. baicalensis , ~90% of genes were mapped, whereas the mapping ratio was <75% in periderm tissue ( Supplementary Data Table S2 ).…”

“…It is important to address the above issues for identifying genes or enzymes with functional characterization based on high­throughput omics data screening. The genome and transcriptome of S. baicalensis have been sequenced and extensively characterized over the past 10 years [ 14 , 18 , 29 – 31 ]. Limited studies of the proteome as the main executer of most biological processes in S. baicalensis have yielded promising insights.…”

Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs

“…The genome, protein and annotation files of S. baicalensis were downloaded from the National Genomics Data Center ( https://ngdc.cncb.ac.cn/search/?dbId=gwh&q=PRJCA009554&page=1 , Accessed on September 20, 2022) (Hu et al 2022 ). Hidden Markov Model (HMM) seed files for SBP domains were downloaded from the Pfam database ( http://pfam.sanger.ac.uk/ , Accessed on 20 September 2022) (Punta et al 2012 ).…”

“…Raw RNA-seq data for roots, stems, leaves, and flowers were downloaded from the European Nucleotide Archive ( https://www.ebi.ac.uk/ena/browser/view/PRJNA263255 ) (Hu et al 2022 ). Sequences were requalified using fastp to filter out low-quality and linker sequences (Chen et al 2018 ).…”

Melatonin: A biomolecule for mitigating postharvest chilling injury in fruits and vegetables

“…However, many plant families possess MT, and the maximum plant species identified having high concentrations of MT belong to the Rosaceae , Brassicaceae , Poaceae , Vitaceae , and Apiaceae families (Nawaz et al., 2016). A high MT concentration of about 710 ng/g was also found in the roots of Huang‐qin, Scutellaria biacalensis , belonging to the Lamiaceae family (Hu et al., 2022). As many species are unstudied, there may be a possibility of the presence of even higher amounts of MT.…”