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Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion.

ABSTRACT: Allium sect. Cepa (Amaryllidaceae) comprises economically important plants, yet resolving the phylogenetic relationships within the section has been difficult as nuclear and chloroplast-based phylogenetic trees have been incongruent. Until now, phylogenetic studies of the section have been based on a few genes. In this study, we sequenced the complete chloroplast genome (plastomes) of four central Asian species of sect. Cepa: Allium oschaninii, A. praemixtum, A. pskemense and A. galanthum. Their chloroplast (cp) genomes included 114 unique genes of which 80 coded proteins. Seven protein-coding genes were highly variable and therefore promising for future phylogenetic and phylogeographic studies. Our plastome-based phylogenetic tree of Allium sect. Cepa revealed two separate clades: one comprising the central Asian species A. oschaninii, A. praemixtum, and A. pskemense, and another comprising A. galanthum, A. altaicum, and two cultivated species, A. cepa and A. fistulosum. These findings contradict previously reported phylogenies that relied on ITS and morphology. Possible explanations for this discrepancy are related to interspecific hybridization of species ancestral to A. galanthum and A. cepa followed by chloroplast capture; however, this is impossible to prove without additional data. Our results suggest that the central Asian Allium species did not play a role in the domestication of the common onion. Among the chloroplast genes, rpoC2 was identified as a gene of choice in further phylogeographical studies of the genus Allium.

SUBMITTER: Yusupov Z

PROVIDER: S-EPMC8103341 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundOnion waste was reported to be a valuable source of bioactive constituents with potential health-promoting benefits. This sparked a surge of interest among scientists for its valorization. This study aims to investigate the chemical profiles of peel and root extracts of four onion cultivars (red, copper-yellow, golden yellow and white onions) and evaluate their erectogenic and anti-inflammatory potentials.MethodsUPLC-QqQ-MS/MS analysis and chemometric tools were utilized to determine the chemical profiles of onion peel and root extracts. The erectogenic potential of the extracts was evaluated using the PDE-5 inhibitory assay, while their anti-inflammatory activity was determined by identifying their downregulating effect on the gene expression of IL-6, IL-1β, IFN-γ, and TNF-α in LPS-stimulated WBCs.ResultsA total of 103 metabolites of diverse chemical classes were identified, with the most abundant being flavonoids. The organ's influence on the chemical profiles of the samples outweighed the influence of the cultivar, as evidenced by the close clustering of samples from the same organ compared to the distinct separation of root and peel samples from the same cultivar. Furthermore, the tested extracts demonstrated promising PDE-5 and anti-inflammatory potentials and effectively suppressed the upregulation of pro-inflammatory markers in LPS-stimulated WBCs. The anti-inflammatory activities exerted by peel samples surpassed those of root samples, highlighting the importance of selecting the appropriate organ to maximize activity. The main metabolites correlated with PDE-5 inhibition were cyanidin 3-O-(malonyl-acetyl)-glucoside and quercetin dimer hexoside, while those correlated with IL-1β inhibition were γ-glutamyl-methionine sulfoxide, γ-glutamyl glutamine, sativanone, and stearic acid. Taxifolin, 3'-hydroxymelanettin, and oleic acid were highly correlated with IL-6 downregulation, while quercetin 4'-O-glucoside, isorhamnetin 4'-O-glucoside, and p-coumaroyl glycolic acid showed the highest correlation to IFN-γ and TNF-α inhibition.ConclusionThis study provides a fresh perspective on onion waste as a valuable source of bioactive constituents that could serve as the cornerstone for developing new, effective anti-PDE-5 and anti-inflammatory drug candidates.

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Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion.

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