Stevia rebaudiana Bertoni is popular source of plant-derived low/no-calorie natural sweeteners (LNCSs), collectively known as steviol glycosides (SGs). Nevertheless, genetic predisposition for targeted biosynthesis of SGs is complex due to multi-substrate functionality of key uridine diphosphate glycosyltransferases (UGTs). Here, we created a high-quality monoploid assembly of 1.34 Gb with N50 value of 110 Mb, 55 551 predicted protein-coding genes, and ~80% repetitive regions in Rebaudioside-A (Reb-A) enriched cultivar of S. rebaudiana. Additionally, a haplotype-based chromosome assembly consisting of haplotype A and haplotype B with an overall genome size of 2.33Gb was resolved, harbouring 639 634 variants including single nucleotide polymorphisms (SNPs), indels and structural variants (SVs). Furthermore, a lineage-specific whole genome duplication analysis revealed that gene families encoding UGTs and Cytochrome-P450 (CYPs) were tandemly duplicated. Additionally, expression analysis revealed five tandemly duplicated gene copies of UGT76G1 having significant correlations with Reb-A content, and identified key residue (leu200val) in the glycosylation of Reb-A. Furthermore, missense variations identified in the acceptor region of UGT76G1 in haplotype resolve genome, transcriptional and molecular docking analysis were confirmed with resequencing of 10 diverse stevia genotypes (~25X). Gene regulatory network analysis identified key transcription factors (MYB, bHLH, bZIP and AP2-ERF) as potential regulators of SG biosynthesis. Overall, this study provides haplotype-resolved chromosome-level genome assembly for genome editing and enhancing breeding efforts for targeted biosynthesis of SGs in S. rebaudiana.

中文翻译：

---

高质量的单倍型解析染色体组装提供了进化见解和甜菊糖苷 (SG) 生物合成的目标


甜叶菊是植物源性低/无热量天然甜味剂 (LNCS) 的流行来源，统称为甜菊糖苷 (SG)。然而，由于关键尿苷二磷酸糖基转移酶 (UGT) 的多底物功能，SG 靶向生物合成的遗传倾向很复杂。在这里，我们在莱鲍迪苷 A (Reb-A) 富集的莱鲍迪安娜品种中创建了 1.34 Gb 的高质量单倍体组装体，N50 值为 110 Mb、55 551 个预测的蛋白质编码基因和约 80% 的重复区域。此外，还解析了由单倍型 A 和单倍型 B 组成的基于单倍型的染色体组装，总基因组大小为 2.33Gb，包含 639 634 个变异，包括单核苷酸多态性 (SNP)、插入缺失和结构变异 (SV)。此外，谱系特异性全基因组重复分析表明，编码 UGT 和细胞色素-P450 (CYP) 的基因家族是串联重复的。此外，表达分析揭示了UGT76G1的五个串联重复基因拷贝与Reb-A含量显着相关，并鉴定了Reb-A糖基化中的关键残基(leu200val)。此外，单倍型解析基因组、转录和分子对接分析中 UGT76G1 受体区域中发现的错义变异通过 10 种不同甜菊基因型的重新测序得到证实 (~25X)。基因调控网络分析确定了关键转录因子（MYB、bHLH、bZIP 和 AP2-ERF）作为 SG 生物合成的潜在调控因子。总体而言，这项研究提供了单倍型解析的染色体水平基因组组装，用于基因组编辑和加强育种工作，以实现雷鲍迪安娜 SG 的靶向生物合成。