The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesis

Abstract

Stevia (Stevia rebaudiana Bertoni) is well known for its very sweet steviol glycosides (SGs) consisting of a common tetracyclic diterpenoid steviol backbone and a variable glycone. Steviol glycosides are 150–300 times sweeter than sucrose and are used as natural zero-calorie sweeteners. However, the most promising compounds are biosynthesized in small amounts. Based on Illumina, PacBio, and Hi-C sequencing, we constructed a chromosome-level assembly of Stevia covering 1416 Mb with a contig N50 value of 616.85 kb and a scaffold N50 value of 106.55 Mb. More than four-fifths of the Stevia genome consisted of repetitive elements. We annotated 44,143 high-confidence protein-coding genes in the high-quality genome. Genome evolution analysis suggested that Stevia and sunflower diverged ~29.4 million years ago (Mya), shortly after the whole-genome duplication (WGD) event (WGD-2, ~32.1 Mya) that occurred in their common ancestor. Comparative genomic analysis revealed that the expanded genes in Stevia were mainly enriched for biosynthesis of specialized metabolites, especially biosynthesis of terpenoid backbones, and for further oxidation and glycosylation of these compounds. We further identified all candidate genes involved in SG biosynthesis. Collectively, our current findings on the Stevia reference genome will be very helpful for dissecting the evolutionary history of Stevia and for discovering novel genes contributing to SG biosynthesis and other important agronomic traits in future breeding programs.

Transcriptomic Characterization of Nitrate-Enhanced Stevioside Glycoside Synthesis in Stevia (Stevia rebaudiana) Bertoni

“…In contrast, the SrDXS and SrDXR families were upregulated by NO 3 − , suggesting that these genes contributed to increased SGs synthesis, with their function in mediating metabolic flow into the MEP pathway. This aligns with MEP being the main pathway in providing the 5-carbon isoprenoid unit for SG biosynthesis [29,51]. Even more striking was the upregulation of genes encoding GGPPS and CPS, by NO 3 − feeding.…”

“…In addition, the frequency of >30 Phred quality score (Q30) was higher than 94.27% and the guanine-cytosine (GC) content was higher than 45.42% for all the samples, indicating that the sequence data were of high quality. Then, 60.45-76.30% of the clean reads were mapped to the reference genome of stevia plants (https://doi.org/10.6084/m9.figshare.14169491.v1 (accessed on 5 March 2021)) [29], and 48.83-62.55% of the clean reads were uniquely mapped onto the stevia genome. In total, 35,424 and 36,063 genes were expressed (FPKM > 0) in the A-N and N-N treatments, respectively (Supplemental Table S1).…”

“…The high-quality clean-read data were obtained by removing reads containing adapter contamination and eliminating the low-quality reads. HISAT 2 program and StringTie were used for the reads mapping and assembly [76,77], with the genome data of stevia referenced for further annotation [29]. Functional annotation of all identified genes was performed through NCBI nonredundant protein sequences, nonredundant nucleotide sequences, SwissProt, Gene Ontology (GO), Clusters of Orthologous Groups of proteins (KOG/COG) and the Kyoto Encyclopedia of Genes and Genomes (KEGG).…”

Glycosyltransferases: Mining, engineering and applications in biosynthesis of glycosylated plant natural products

“…Genomic analysis of whole genome sequence data can provide a multi-level resource for mining novel enzymes that can be greatly informative for researchers seeking to identify genes involved in glycosylated PNP synthesis [ [59] , [60] , [61] ]. Huang et al.…”

Genome assembly and analysis of the flavonoid and phenylpropanoid biosynthetic pathways in Fingerroot ginger (Boesenbergia rotunda)

“…Genomic level studies improve understanding of the biology and biochemistry of the plant and can be applied in breeding for improved agronomy and plant products. Whole genome sequencing identifies genes and regulatory sequences for complex biological processes such as secondary metabolite biosynthesis 43,44,45 , while transcriptional profiling provides information for functional studies. Structural genomic studies have been undertaken in other Zingiberales including turmeric (Curcuma longa; genome size of 1.24 Gb) 46 and for several Musaceae species and cultivars, which have genome sizes ranging from 462 Mb to 598 Mb (Banana Genome Hub https://banana-genome-hub.southgreen.fr/) 47 ; while the Pan-genome of Musa Ensete has a genome size of 951.6 Mb 48 .…”