Multi-Omics Analyses Uncover the Mechanism Underlying Polyploidization-Enhanced Steviol Glycosides Biosynthesis in Stevia rebaudiana
Abstract
:1. Introduction
2. Results
2.1. Differentially Accumulated Metabolites (DAMs) in Stevia Post-Polyploidization
2.2. Differentially Expressed Genes (DEGs) in Stevia Post-Polyploidization
2.3. Integrative Transcriptome and Metabolome Analysis Revealed the Enhanced SG Biosynthesis in Stevia Post-Polyploidization
2.4. Taxonomic Features of the Rhizosphere Microbes of Diploid and Autotetraploid Stevia
2.5. Multi-Omics Network Analysis of the Microbe–Gene–Metabolite Associations
3. Discussion
3.1. Steviol Glycosides Biosynthesis Mechanism Elucidated through Integrated Transcriptome and Metabolome Analysis
3.2. Optimized Rhizosphere Microbiome Contributes to SG Biosynthesis in Autotetraploid Stevia
4. Materials and Methods
4.1. Plant Materials
4.2. Total RNA Extraction, Library Preparation, and Transcriptome Sequencing
4.3. Transcriptome Assembly, Differential Expression, and Functional Enrichment Analysis
4.4. qRT-PCR Analysis
4.5. Metabolite Measurements and Analysis
4.6. Rhizosphere Microbial DNA Extraction and Amplicon Sequencing
4.7. Microbial Data Analysis
4.8. Multi-Omics Integrative Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Compounds | Log2FC | VIP |
---|---|---|
Terpenoids | ||
3β,21β,24-trihydroxyserrat-14-en-29-oic acid-3β(4-hydroxy-3-methoxybenzoate) | 18.8 | 1.5 |
Steviol | 16.8 | 1.5 |
Ent-kaurenal | 1.9 | 1.3 |
Rebaudioside A | 0.9 | 1.4 |
Steviolbioside | 0.8 | 1.0 |
Rebaudioside C | 0.6 | 0.9 |
Phenolic acids | ||
3-(4-hydroxyphenyl)-propionic acid | 10.1 | 1.5 |
(S)-2-phenyloxirane | 2.4 | 1.4 |
1-O-feruloyl-3-O-p-coumaroylglycerol | 3.1 | 1.3 |
5-O-caffeoylshikimic acid | 2.1 | 1.4 |
Galloyl methyl gallate | 2.0 | 1.2 |
3-O-feruloylquinic acid | 1.82 | 1.37 |
Lipids | ||
9,10-dihydroxy-12,13-epoxyoctadecanoic acid | 4.4 | 1.4 |
Dihydrosphingosine-1-phosphate | 3.4 | 1.3 |
3-dehydrosphinganine | 2.3 | 1.3 |
Phytosphingosine | 2.1 | 1.3 |
LysoPC 18:1 | 1.6 | 1.3 |
LysoPE 18:0 | 1.7 | 1.2 |
1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine | 1.7 | 1.2 |
LysoPE 16:1 | 1.6 | 1.1 |
LysoPE 16:1 | 2.0 | 1.1 |
Flavonoids | ||
Syringetin | 16.7 | 1.5 |
Quercetin-3-O-(2″-O-rhamnosyl) rutinoside-7-O-glucoside | 10.7 | 1.4 |
Cirsiliol | 9.9 | 1.4 |
Cirsimaritin | 9.3 | 1.5 |
3′,4′-dihydroxy-7,5′-dimethoxyflavone | 9.8 | 1.4 |
Quercetin-3,3′-dimethyl ether | 8.1 | 1.4 |
5,7,2′,5′-tetrahydroxy-8,6′-dimethoxyflavone | 9.2 | 1.4 |
3,7-dimethylquercetagetin-(3′,4′,5,6-Tetrahydroxy-3,7-dimethoxyflavone) | 8.8 | 1.4 |
Rhamnetin; 3,5,3′,4′-tetrahydroxy-7-methoxyflavone | 8.0 | 1.5 |
Alkaloids | ||
Tryptamine | 4.9 | 1.4 |
N-caffeoylputrescine | 3.6 | 1.4 |
Retronecine | 2.7 | 1.4 |
2-phenylethylamine | 2.7 | 1.4 |
Vitamin | ||
Retinol | 1.4 | 1.4 |
Nicotinamide | 1.0 | 1.4 |
Riboflavin | 2.0 | 1.4 |
Biotin | 2.2 | 1.4 |
Others | ||
2-phenylethanol | 2.2 | 1.4 |
Dipteryxin | 9.01 | 1.45 |
2-Dehydro-3-deoxy-L-arabinonate | 2.14 | 1.45 |
D-Threose | 2.42 | 1.43 |
ID | Name | Log2FC | ID | Name | Log2FC |
---|---|---|---|---|---|
WRKY | Streb.2G002460 | BZP23_ARATH | 1.9 | ||
Streb.8G004280 | WRK21_ARATH | 2.0 | Streb.4G010840 | CPRF2_PETCR | 1.3 |
Streb.11G007600 | WRK22_ARATH | 1.8 | Streb.7G020660 | GBF1_ARATH | 1.2 |
Streb.1G002040 | WRK70_SOLLC | 1.8 | Streb.3G007530 | BZIP9_ARATH | −3.1 |
Streb.3G012150 | WRKY6_ARATH | 1.6 | Streb.3G012510 | AI5L4_ARATH | −2.1 |
Streb.4G015740 | WRKY4_ARATH | −2.5 | Streb.8G015740 | VIP1_ARATH | −1.0 |
Streb.2G030570 | WRK51_ARATH | −1.4 | bHLH | ||
Streb.4G005140 | WRK65_ARATH | −1.4 | Streb.Contig05035G000020 | ILR3_ARATH | 6.1 |
Streb.2G051870 | WRK40_ARATH | −1.3 | Streb.2G020970 | BIM2_ARATH | 4.3 |
NAC | Streb.1G023980 | IRO2_ORYSI | 3.9 | ||
Streb.8G026410 | NAC83_ARATH | 9.2 | Streb.1G024080 | ORG3_ARATH | 3.8 |
Streb.10G007870 | NTL9_ARATH | 1.9 | Streb.4G026850 | BH087_ARATH | 3.8 |
Streb.5G033120 | NAC75_ARATH | 1.3 | Streb.10G018330 | BH128_ARATH | 3.2 |
Streb.9G020010 | NAC73_ARATH | 1.3 | Streb.2G013370 | BH094_ARATH | 2.4 |
Streb.8G033830 | NAC17_ARATH | 1.3 | Streb.2G028430 | RHL1_LOTJA | 1.4 |
Streb.10G019010 | NAC43_ARATH | 1.2 | Streb.9G004040 | MYC2_ARATH | 1.3 |
Streb.2G020770 | NAC2_ARATH | −3.0 | Streb.2G055730 | BIM1_ARATH | 1.3 |
Streb.5G025450 | NAC6_SOYBN | −1.6 | Streb.11G016670 | ICE1_ARATH | 1.3 |
Streb.7G009790 | NAC91_ARATH | −1.2 | Streb.11G003730 | BH030_ARATH | 1.1 |
MYB | Streb.6G032180 | UNE10_ARATH | −2.5 | ||
Streb.10G031370 | MY111_ARATH | 8.1 | Streb.7G020980 | BH025_ARATH | −1.9 |
Streb.11G027310 | MYB4_ORYSJ | 4.0 | Streb.3G020800 | BH153_ARATH | −1.7 |
Streb.11G030580 | KUA1_ARATH | 2.0 | Streb.4G022320 | PIF7_ARATH | −1.5 |
Streb.6G002150 | MB101_ARATH | 1.9 | AP2/ERF | ||
Streb.7G028220 | RVE8_ARATH | 1.8 | Streb.5G008600 | AP21_ORYSI | 4.2 |
Streb.11G013850 | MYB90_ARATH | 1.7 | Streb.8G009050 | AP23_ORYSI | 3.3 |
Streb.2G049910 | MYB06_ANTMA | 1.3 | Streb.11G011700 | ERF34_ARATH | 1.7 |
Streb.4G021750 | MYBS1_ORYSI | 1.1 | Streb.4G000620 | ERF54_ARATH | 1.5 |
Streb.2G045880 | LHY_PETHY R | 1.1 | Streb.5G004440 | EF118_ARATH | 1.5 |
Streb.1G015820 | MYB44_ARATH | −1.9 | Streb.1G037650 | DREB3_ARATH | 1.4 |
Streb.9G001240 | MYB38_MAIZE | −1.9 | Streb.9G000120 | ERF39_ARATH | 1.1 |
Streb.2G021360 | MYB1_ACTCC | −1.9 | Streb.10G004210 | EF102_ARATH | 1.1 |
Streb.9G010620 | MYB48_ARATH | −1.6 | Streb.Contig03456G000010 | ERF61_ARATH | −2.1 |
Streb.9G019430 | MY102_ARATH | −1.2 | Streb.10G009110 | RAP23_ARATH | −1.5 |
Streb.1G000660 | MYB17_ARATH | −1.0 | Streb.4G017620 | ERF08_ARATH | −1.5 |
bZIP | Streb.4G017600 | AP2_ARATH | −1.2 | ||
Streb.9G027550 | BZP44_ARATH | 6.1 | Streb.6G008530 | ERF3_TOBAC | −1.0 |
Streb.10G008960 | BZP16_ARATH | 2.8 |
ID | Name | log2FC | ID | Name | log2FC |
---|---|---|---|---|---|
Ion transport protein | ABC transporter | ||||
Streb.3G013310 | CNGC2_ARATH | 3.1 | Streb.1G035320 | AB39G_ARATH | 4.2 |
Streb.2G032360 | CNGC2_ARATH | 1.2 | Streb.3G009500 | AB10I_ARATH | 3 |
Streb.7G022990 | CNGC1_ARATH | −1.2 | Streb.5G025360 | AB11G_ARATH | 2.4 |
Sugar (and other) transporter | Streb.5G001490 | AB3C_ARATH | 1.8 | ||
Streb.9G006200 | EDL16_ARATH | 2.1 | Streb.4G013640 | AB26B_ARATH | 1.4 |
Streb.9G025500 | STP13_ARATH | 1.0 | Streb.1G016980 | AB5G_ARATH | 1.2 |
Streb.10G002460 | PHT11_PETHY | −2.3 | Streb.3G008960 | AB3C_ARATH | 1.0 |
Streb.2G008870 | EDL16_ARATH | −1.6 | Streb.9G030840 | ABCG1_PETHY | −2.2 |
ZIP Zinc transporter | Streb.10G006460 | AB10C_ARATH | −1.7 | ||
Streb.Contig03477G000010 | ZIP6_ARATH | 5.6 | Streb.10G027430 | AB20G_ARATH | −1.3 |
Streb.6G017260 | ZIP2_ARATH | 5.7 | Triose-phosphate Transporter | ||
Streb.1G047870 | ZIP6_ARATH | −2.6 | Streb.6G014120 | UGNT1_ARATH | 2.5 |
Streb.10G018100 | IRT3_ARATH | −1.7 | Streb.5G032270 | GFT1_ARATH | 2.3 |
CorA-like Mg2+ transporter protein | Streb.5G022800 | GPT1_ARATH | 1.6 | ||
Streb.2G000140 | MRS23_ARATH | 6.6 | Streb.9G009400 | UUAT1_ARATH | 1.2 |
Streb.9G031220 | MRS23_ARATH | 3.6 | Sugar efflux transporter for intercellular exchange | ||
Streb.11G025820 | MRS24_ARATH | 1.3 | Streb.11G000040 | NOD3_MEDTR | 1.4 |
Transmembrane amino acid transporter protein | Streb.1G032140 | SWET1_ARATH | 1.4 | ||
Streb.2G034940 | AAP6_ARATH | 2.3 | Streb.2G031580 | SWT17_ARATH | 1.1 |
Streb.9G013250 | LAX4_MEDTR | 1.1 | Streb.8G017430 | SWET3_ARATH | −1.1 |
Streb.2G018370 | LHT1_ARATH | −1.9 |
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Liu, J.; Wang, J.; Chen, M.; Meng, W.; Ding, A.; Chen, M.; Ding, R.; Tan, M.; Xiang, Z. Multi-Omics Analyses Uncover the Mechanism Underlying Polyploidization-Enhanced Steviol Glycosides Biosynthesis in Stevia rebaudiana. Plants 2024, 13, 2542. https://doi.org/10.3390/plants13182542
Liu J, Wang J, Chen M, Meng W, Ding A, Chen M, Ding R, Tan M, Xiang Z. Multi-Omics Analyses Uncover the Mechanism Underlying Polyploidization-Enhanced Steviol Glycosides Biosynthesis in Stevia rebaudiana. Plants. 2024; 13(18):2542. https://doi.org/10.3390/plants13182542
Chicago/Turabian StyleLiu, Juan, Jiaxue Wang, Mingjia Chen, Wenna Meng, Anping Ding, Miao Chen, Rongping Ding, Mingpu Tan, and Zengxu Xiang. 2024. "Multi-Omics Analyses Uncover the Mechanism Underlying Polyploidization-Enhanced Steviol Glycosides Biosynthesis in Stevia rebaudiana" Plants 13, no. 18: 2542. https://doi.org/10.3390/plants13182542