Study of regulatory elements in promoter regions of co-expressed genes in tomato when facing low temperatures

Heidari, Parviz; Nussbaumer, Thomas

doi:10.30473/cb.2018.5108

Study of regulatory elements in promoter regions of co-expressed genes in tomato when facing low temperatures

Document Type : Research Paper

Authors

Parviz Heidari ¹
Thomas Nussbaumer ²

¹ Assistant Professor, Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran.

² Postdoc Researcher, INET Institute, Munchen, Germany.

10.30473/cb.2018.5108

Abstract

Next-generation sequencing (NGS) techniques such as RNA-Seq can provide expression information per gene and can be used to construct co-expression networks. These networks can produce valuable information to understand plant responses when facing environmental changes. In this study, a complete profile of tomato gene expressions under low temperature treatment was analyzed by “Weighted Gene Co-expression Network Analysis”. The clustering results allowed to group 20,267 genes into eight modules. The results of Gene ontology (GO) term analysis highlighted different functions between co-expression groups in terms of biological process and molecular function. Accordingly, the first module overrepresented to heat shock proteins (HSPs). Protein kinases and proteins involved in post-translational modification were in the second and third modules, respectively. The promoter of genes in fifth module was screened according to the different expression patterns in the tomato genotypes. The cis-elements such as ACGTG and TTGAC were observed in promoter site of all genes. The transcription factor families of AP2 / ERF and ZF-HD have the highest binding status in promoter of genes of the fifth module. The results present the key cis-regulatory elements that effect on co-expressed genes network and involve in anti-oxidant process under cold stress.

Keywords

20.1001.1.22520783.1397.8.23.2.8

Main Subjects

Bioinformatics

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