Please cite this article in press as: Saha, J., et al., Genome-wide analysis and evolutionary study of sucrose non- fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza. Comput. Biol. Chem. (2013), http://dx.doi.org/10.1016/j.compbiolchem.2013.09.005 ARTICLE IN PRESS G Model CBAC-6293; No. of Pages 12 Computational Biology and Chemistry xxx (2013) xxx–xxx Contents lists available at ScienceDirect Computational Biology and Chemistry jo ur nal ho me pag e: www.elsevier.com/locate/compbiolchem Research Article Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza Jayita Saha a,b,1 , Chitrita Chatterjee a,1 , Atreyee Sengupta a,b , Kamala Gupta b,∗ , Bhaskar Gupta a,∗∗ a Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India b Department of Biological Sciences (Section Botany), Presidency University, 86/1 College Street, Kolkata 700073, India a r t i c l e i n f o Article history: Received 26 April 2013 Received in revised form 27 September 2013 Accepted 27 September 2013 Keywords: Abiotic stress Phylogenetic tree Promoter element SNF1-related protein kinase 2 SnRK2 a b s t r a c t The over-expression of plant specific SnRK2 gene family members by hyperosmotic stress and some by abscisic acid is well established. In this report, we have analyzed the evolution of SnRK2 gene fam- ily in different plant lineages including green algae, moss, lycophyte, dicot and monocot. Our results provide some evidences to indicate that the natural selection pressure had considerable influence on cis-regulatory promoter region and coding region of SnRK2 members in Arabidopsis and Oryza indepen- dently through time. Observed degree of sequence/motif conservation amongst SnRK2 homolog in all the analyzed plant lineages strongly supported their inclusion as members of this family. The chromosomal distributions of duplicated SnRK2 members have also been analyzed in Arabidopsis and Oryza. Massively Parallel Signature Sequencing (MPSS) database derived expression data and the presence of abiotic stress related promoter elements within the 1 kb upstream promoter region of these SnRK2 family members further strengthen the observations of previous workers. Additionally, the phylogenetic relationships of SnRK2 have been studied in all plant lineages along with their respective exon–intron structural patterns. Our results indicate that the ancestral SnRK2 gene of land plants gradually evolved by duplication and diversification and modified itself through exon–intron loss events to survive under environmental stress conditions. © 2013 Elsevier Ltd. All rights reserved. 1. Introduction Plants have acquired several adaptive features to survive against abiotic stresses, such as temperature, UV irradiation, drought, salinity, pH variation, high light intensity and rising atmospheric pollutant levels that have severely affected crop growth and qual- ity (Mattoo et al., 2000; Basra, 2001; Serraj and Sinclair, 2002; Xiong and Zhu, 2002; Long et al., 2006). The adverse effect of most of these stresses lead to the osmotic stress, ionic imbalance, DNA and/or protein damage and many other harmful physiological phenotypes Abbreviations: ABA, abscisic acid; ABRE, abscisic acid responsive element; CDS, coding sequences; DRE/CRT, dehydration-responsive element; IRO2, iron- responsive element; LTRE, low temperature responsive element; PRE, pro- or hypo-osmolarity-responsive element; SNF-1, sucrose non-fermenting protein 1; SnRK2, SNF1-related protein kinase 2; SURE, sulfur-responsive element. ∗ Corresponding author. Tel.: +91 9831806738. ∗∗ Corresponding author. Tel.: +91 9831128734; fax: +91 033 2257 2444. E-mail addresses: kamala.botany@presiuniv.ac.in, kamalagupta@gmail.com (K. Gupta), bhaskarzoology@gmail.com, bhaskarzoology@gmail.com (B. Gupta). 1 Joint 1st author (equal contribution). (Serraj and Sinclair, 2002). Plants that perceive these extracellu- lar environmental cues modulate intracellular signaling cascades and facilitate genetic, biochemical and physiological changes to cope up with such myriad stresses (Finkelstein et al., 2002; Zhu, 2002; Chinnusamy et al., 2004; Cao et al., 2007; Gupta et al., 2013). The plants that do not have such protective machinery eventually perish. The sucrose non-fermenting 1-related protein kinase (SnRK), homologous to yeast SNF1 genes and mammal AMP-activated pro- tein kinase (AMPK), have been found to be widely distributed in plants and act as key switches in sugar signaling, biotic and abi- otic stresses, seed germination and seedling growth (Chevalier and Walker, 2005; Xue-Fei et al., 2012). Plant SNF-1 related protein kinases have been categorized into three sub-families: SnRK1, SnRK2 and SnRK3 (Wang et al., 2010). SnRK1 complex is a heterotrimeric complex composed of ,  and -subunits containing N-terminal kinase domain and C-terminal regulatory domain that are involved in global regulation of carbon and nitro- gen metabolism (Shukla and Mattoo, 2008; Xue-Fei et al., 2012). SnRK2 subfamily has previously been reported to have kinase domain, ATP binding domain, serine/threonine active site and four 1476-9271/$ – see front matter © 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.compbiolchem.2013.09.005