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Simoni S, Vangelisti A, Clemente C, Usai G, Santin M, Ventimiglia M, Mascagni F, Natali L, Angelini LG, Cavallini A, Tavarini S, Giordani T. Transcriptomic Analyses Reveal Insights into the Shared Regulatory Network of Phenolic Compounds and Steviol Glycosides in Stevia rebaudiana. Int J Mol Sci 2024; 25:2136. [PMID: 38396813 PMCID: PMC10889303 DOI: 10.3390/ijms25042136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Stevia rebaudiana (Bertoni) is a highly valuable crop for the steviol glycoside content in its leaves, which are no-calorie sweeteners hundreds of times more potent than sucrose. The presence of health-promoting phenolic compounds, particularly flavonoids, in the leaf of S. rebaudiana adds further nutritional value to this crop. Although all these secondary metabolites are highly desirable in S. rebaudiana leaves, the genes regulating the biosynthesis of phenolic compounds and the shared gene network between the regulation of biosynthesis of steviol glycosides and phenolic compounds still need to be investigated in this species. To identify putative candidate genes involved in the synergistic regulation of steviol glycosides and phenolic compounds, four genotypes with different contents of these compounds were selected for a pairwise comparison RNA-seq analysis, yielding 1136 differentially expressed genes. Genes that highly correlate with both steviol glycosides and phenolic compound accumulation in the four genotypes of S. rebaudiana were identified using the weighted gene co-expression network analysis. The presence of UDP-glycosyltransferases 76G1, 76H1, 85C1, and 91A1, and several genes associated with the phenylpropanoid pathway, including peroxidase, caffeoyl-CoA O-methyltransferase, and malonyl-coenzyme A:anthocyanin 3-O-glucoside-6″-O-malonyltransferase, along with 21 transcription factors like SCL3, WRK11, and MYB111, implied an extensive and synergistic regulatory network involved in enhancing the production of such compounds in S. rebaudiana leaves. In conclusion, this work identified a variety of putative candidate genes involved in the biosynthesis and regulation of particular steviol glycosides and phenolic compounds that will be useful in gene editing strategies for increasing and steering the production of such compounds in S. rebaudiana as well as in other species.
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Affiliation(s)
- Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Clarissa Clemente
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Marco Santin
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Maria Ventimiglia
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Lucia Natali
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Luciana G. Angelini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
- Interdepartmental Research Centre “Nutraceuticals and Food for Health—NUTRAFOOD”, University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
| | - Silvia Tavarini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
- Interdepartmental Research Centre “Nutraceuticals and Food for Health—NUTRAFOOD”, University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124 Pisa, Italy (C.C.); (M.S.); (M.V.); (S.T.)
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Ventimiglia M, Castellacci M, Usai G, Vangelisti A, Simoni S, Natali L, Cavallini A, Mascagni F, Giordani T. Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study. PLANTS (BASEL, SWITZERLAND) 2023; 12:1405. [PMID: 36987093 PMCID: PMC10058865 DOI: 10.3390/plants12061405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/08/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Genome divergence by repeat proliferation and/or loss is a process that plays a crucial role in species evolution. Nevertheless, knowledge of the variability related to repeat proliferation among species of the same family is still limited. Considering the importance of the Asteraceae family, here we present a first contribution towards the metarepeatome of five Asteraceae species. A comprehensive picture of the repetitive components of all genomes was obtained by genome skimming with Illumina sequence reads and by analyzing a pool of full-length long terminal repeat retrotransposons (LTR-REs). Genome skimming allowed us to estimate the abundance and variability of repetitive components. The structure of the metagenome of the selected species was composed of 67% repetitive sequences, of which LTR-REs represented the bulk of annotated clusters. The species essentially shared ribosomal DNA sequences, whereas the other classes of repetitive DNA were highly variable among species. The pool of full-length LTR-REs was retrieved from all the species and their age of insertion was established, showing several lineage-specific proliferation peaks over the last 15-million years. Overall, a large variability of repeat abundance at superfamily, lineage, and sublineage levels was observed, indicating that repeats within individual genomes followed different evolutionary and temporal dynamics, and that different events of amplification or loss of these sequences may have occurred after species differentiation.
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