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Article|01 Jun 2021|OPEN
The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesis
Xiaoyang Xu1, Haiyan Yuan1, Xiaqing Yu2, Suzhen Huang1, Yuming Sun1, Ting Zhang1, Qingquan Liu1, Haiying Tong1, Yongxia Zhang1, Yinjie Wang1, Chunxiao Liu3, Lei Wu4, Menglan Hou1 & Yongheng Yang1,
1Institute of Botany, Jiangsu Province and Chinese Academy of Sciences/ Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014 Jiangsu, China
2College of Horticulture, Nanjing Agricultural University, Nanjing 210095 Jiangsu, China
3Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014 Jiangsu, China.
4Biomarker Technologies Corporation, Beijing 101300, China

Horticulture Research 8,
Article number: 129 (2021)
doi: 10.1038/hortres.2021.129
Views: 220

Received: 23 Nov 2020
Revised: 07 Mar 2020
Accepted: 14 Mar 2021
Published online: 01 Jun 2021


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.