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. 2021 Jan 12;11(1):768.
doi: 10.1038/s41598-020-80837-6.

Transcriptome and phytochemical analyses provide insights into the organic sulfur pathway in Allium hirtifolium

Aboozar Soorni  1 , Amir Mohammad Akrami  2 , Reza Abolghasemi  3 , Maryam Vahedi  4
Affiliations

Transcriptome and phytochemical analyses provide insights into the organic sulfur pathway in Allium hirtifolium

Aboozar Soorni et al. Sci Rep. .

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Top 20 families of differentially expressed transcription factors in three main comparison of flower vs. stem, bulb vs. stem, and bulb vs. flower.
Figure 2
Figure 2
Biological process ontology of the differentially expressed genes identified among tissues comparison. F, S, and B represent flower, stem and bulb tissues, respectively. Here, U represents up-regulated term.
Figure 3
Figure 3
Overview of KEGG pathway maps of DEGs defined by KAAS. Bars represent the number of assignments of unigenes to each term.
Figure 4
Figure 4
Expression patterns of unigenes involved in the organic sulfur pathway. F, S, and B represent flower, stem, and bulb tissues, respectively. The red and green circles represent up-regulated and down-regulated DEGs, respectively.
Figure 5
Figure 5
Confirmation of the transcriptome sequencing data by quantitative real-time (qRT)-PCR. Nine differentially expressed genes (DEGs) involved in sulfur pathway.
Figure 6
Figure 6
Heatmap of differentially expressed Alliinase genes family.
Figure 7
Figure 7
Phylogenetic relationships among Allium species inferred from cpDNA data.
Figure 8
Figure 8
Tissues of A. hirtifolium used for de novo transcriptome assembly. (A) A. hirtifolium growth habit in nature; (B) stem; (C) flower; (D) and bulb.
See this image and copyright information in PMC

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References

    1. Lorigooini Z, Kobarfard F, Ayatollahi SA. Anti-platelet aggregation assay and chemical composition of essential oil from Allium atroviolaceum Boiss growing in Iran. Int. J. Biosci. (IJB) 2014;5:151–156.
    1. Lanzotti V, Barile E, Antignani V, Bonanomi G, Scala F. Antifungal saponins from bulbs of garlic, Allium sativum L. var. Voghiera. Phytochemistry. 2012;78:126–134. doi: 10.1016/j.phytochem.2012.03.009. - DOI - PubMed
    1. Rose P, Whiteman M, Moore PK, Zhu YZ. Bioactive S-alk (en) yl cysteine sulfoxide metabolites in the genus Allium: The chemistry of potential therapeutic agents. Nat. Product Rep. 2005;22:351–368. doi: 10.1039/b417639c. - DOI - PubMed
    1. Kazemi S, et al. Liver-protective effects of hydroalcoholic extract of Allium hirtifolium boiss. In rats with alloxan-induced diabetes mellitus. ARYA Atheroscl. 2010;6:11. - PMC - PubMed
    1. Mikaili P, Maadirad S, Moloudizargari M, Aghajanshakeri S, Sarahroodi S. Therapeutic uses and pharmacological properties of garlic, shallot, and their biologically active compounds. Iran. J. Basic Med. Sci. 2013;16:1031. - PMC - PubMed

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