Application of data analysis in cold stress: a case study of Nicotiana benthamiana

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dc.contributor.authorKoç, İbrahim
dc.contributor.authorÇalışkaner, Zihni Onur
dc.contributor.authorFiliz, Ertuğrul
dc.date.accessioned2020-04-30T22:39:32Z
dc.date.available2020-04-30T22:39:32Z
dc.date.issued2015
dc.departmentDÜ, Çilimli Meslek Yüksekokulu, Bitkisel ve Hayvansal Üretim Bölümüen_US
dc.descriptionFiliz, Ertugrul/0000-0001-9636-6389en_US
dc.descriptionWOS: 000365331800015en_US
dc.description.abstractCold stress is a major environmental factor in plant life cycles. Nicotiana benthamiana, which belongs to the family Solanaceae, is one of the most commonly used model species in plant-microbe interaction studies. In total, 5205 differentially expressed genes were identified under cold stress in N. benthamiana. Of these, 5029 were upregulated and 176 were downregulated within four time periods (4 h, 12 h, 24 h, and 48 h). The common up- and downregulated genes were identified as 692 and 6, respectively. The functional annotations of these genes were studied and these common genes involved in protein, RNA, miscellaneous enzyme families, signaling, stress, lipid, and carbohydrate metabolisms were enriched by using MapMan ontology. In addition, a total of 22 cold-inducible transcription factors were enriched, including subsets of the zinc finger family, bHLH, E2F/DP, bZIP, SET domain, GRAS, MYB, ARF, CO-like, Homeobox, and DOF zinc finger family members. Our findings will pave the way for understanding the expression of cold-inducible genes as a response to cold stress in Nicotiana species. This study will also be a valuable resource for crop improvement studies under abiotic stress conditions for Nicotiana plants.en_US
dc.description.sponsorshipTUBITAK (the Scientific and Technological Research Council of Turkey)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [1059B141400573]en_US
dc.description.sponsorshipThis study was supported by a grant from TUBITAK (the Scientific and Technological Research Council of Turkey, no. 1059B141400573).en_US
dc.identifier.doi10.3906/bot-1503-25en_US
dc.identifier.endpage+en_US
dc.identifier.issn1300-008X
dc.identifier.issn1303-6106
dc.identifier.issue6en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.startpage1021en_US
dc.identifier.urihttps://doi.org/10.3906/bot-1503-25
dc.identifier.urihttps://hdl.handle.net/20.500.12684/2757
dc.identifier.volume39en_US
dc.identifier.wosWOS:000365331800015en_US
dc.identifier.wosqualityQ3en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakTR-Dizinen_US
dc.language.isoenen_US
dc.publisherTubitak Scientific & Technical Research Council Turkeyen_US
dc.relation.ispartofTurkish Journal Of Botanyen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectSolanaceaeen_US
dc.subjectabiotic stressen_US
dc.subjectgene expressionen_US
dc.subjectdifferentially expressed genesen_US
dc.subjectchilling stressen_US
dc.titleApplication of data analysis in cold stress: a case study of Nicotiana benthamianaen_US
dc.typeArticleen_US

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