TAILIEUCHUNG - Application of data analysis in cold stress: A case study of Nicotiana benthamiana
Cold 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. This study will also be a valuable resource for crop improvement studies under abiotic stress conditions for Nicotiana plants. | Turkish Journal of Botany Turk J Bot (2015) 39: 1021-1032 © TÜBİTAK doi: Research Article Application of data analysis in cold stress: a case study of Nicotiana benthamiana 1,2 1 1 3, İbrahim KOÇ , Zihni Onur ÇALIŞKANER , Ertuğrul FİLİZ * Department of Molecular Biology and Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey 2 Department of Crop Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA 3 Department of Crop and Animal Production, Çilimli Vocational School, Düzce University, Düzce, Turkey Received: Accepted/Published Online: Printed: Abstract: Cold 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. Key words: Solanaceae, abiotic stress, gene expression,
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