Abstract
Allium is one of the well-known genera of the Amaryllidaceae family, which contains over 780 species. Onions, garlic, leeks, and shallots are the most important species of this genus. Allium hirtifolium (shallot) is a rich source of proteins, carbohydrates, lipids, amino acids, and bioactive compounds such as organic sulfur compounds with an expansive range of biological activities and medicinal attributes. To identify the putative compounds and genes involved in the organic sulfur pathway, we applied GC–MS and RNA-seq techniques for the bulb, stem, and flower tissues of A. hirtifolium. The essential oil analysis revealed the maximum amount of sulfur compounds in stem against flower and bulb tissues. Transcriptome profiling showed 6155, 6494, and 4259 DEGs for bulb vs. flower, bulb vs. stem, and flower vs. stem, respectively. Overall, more genes were identified as being up-regulated rather than down-regulated in flower tissue compared to the stem and bulb tissues. Our findings in accordance with other results from different papers, suggest that carbohydrates are vital to bulb formation and development because a high number of identified DEGs (586 genes) were mapped to carbohydrate metabolism. This study has detected the genes in the organic sulfur pathway and indicated that the alliinase gene shows a high variability among different tissues. In general, this study formed a useful genomic resource data to explore tissue-specific sulfur pathway in A. hirtifolium, which is helpful for functional breeding.
Highlights
Allium is one of the well-known genera of the Amaryllidaceae family, which contains over 780 species
All compositions were dominant in aerial parts compared to the bulb, with the most quantity of sulfur compounds found in the stem against the flower and bulb tissues
Dimethyl trisulfide, 2,3,5-trithiahexane, chloromethyl methyl sulfide, and N-butylBenzene sulfonamide, which were the most dominate sulfur compounds identified in tissue culture organs of A. hirtifolium[19], Dipropyl disulfide, and Diisopropyl trisulfide were found to be abundant in the current study
Summary
Allium is one of the well-known genera of the Amaryllidaceae family, which contains over 780 species. To identify the putative compounds and genes involved in the organic sulfur pathway, we applied GC– MS and RNA-seq techniques for the bulb, stem, and flower tissues of A. hirtifolium. This study has detected the genes in the organic sulfur pathway and indicated that the alliinase gene shows a high variability among different tissues. Despite the fact that the pathway of synthesis of the organic sulfur flavor precursors has been deliberated with the assistance of transcriptome sequencing in some Allium species, this technique still can be performed for other species to acquire more knowledge of secondary metabolites biosynthesis, different possible routes for the synthesis of the major flavor precursor, and alliinase genes variation. Genes related to the sulfur pathway, alliinase genes, and the presence of different isoforms in the A. hirtifolium have been discovered for the first time with a novel report for Iranian endemic species
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