Genome wide analysis of NAC gene family ‘sequences’ in sugarcane and its comparative phylogenetic relationship with rice, sorghum, maize and Arabidopsis for prediction of stress associated NAC genes Manimekalai Ramaswamy a, ⁎, Jini Narayanan a , Gokul Manickavachagam a , Selvi Athiappan a , Meena Arun a , Gomathi R b , Bakshi Ram a a Crop Improvement Division, ICAR- Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore 641 007, Tamil Nadu, India b Crop Production Division, ICAR- Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore 641 007, Tamil Nadu, India abstract article info Article history: Received 6 April 2016 Received in revised form 31 October 2016 Accepted 31 October 2016 Available online 2 November 2016 A total of 85 NAC genes of sugarcane (ScNAC) were retrieved from GRASSIUS (grass regulatory information server). An overview of this gene family is presented including conserved domains, phylogenies, compara- tive analysis of NAC genes of sugarcane with its closest relative sorghum and with other monocot species. Among the Poaceae family, the NAC genes from sugarcane showed high sequence identity with most of the NAC genes of Sorghum bicolor. A highly conserved two proline residues, a glycine, phenyl alanine and leucine residues are present in N-terminal domain. Conserved amino acid residues and phylogeny helps us to classify the ScNAC gene family into two major groups (Group I and II) and five subgroups (A–E). The analysis of phylogenetic tree of NAC protein sequences of sugarcane with sorghum, rice, maize and Arabidopsis reveals distinct clades with several orthologs and paralogs. A total of 30 pairs of paralogous NAC genes were identified in sugarcane. Based on the orthology, putative stress associated NAC genes were predicted in sugarcane. These stress associated NAC genes of sugarcane and their orthologs from other species were clustered in the phylogenetic tree and shared common motifs, revealing the possibility of functional similarities within this subgroup. © 2016 Published by Elsevier Inc. Keywords: NAC sugarcane Saccharum Transcription factors 1. Introduction NAC gene family is one of the largest and most important transcrip- tion factors in plants. The term NAC has been derived from three genes sharing common domain (Nac domain). These genes are; NAM (No api- cal meristem), ATAF 1/2 (Arabidopsis transcription activator factor 1/2) and CUC2 (cup shaped cotyledon) (Souer et al., 1996). NAC transcription factors have been implicated in plant growth and development, including flowering (Kim et al., 2007; Sablowski and Meyerowitz, 1998), cell division (Kim et al., 2006), lateral root develop- ment (Xie et al., 2000), leaf senescence (Guo and Gan, 2006; Yang et al., 2011; Podzimska-Sroka et al., 2015), secondary cell wall biosynthesis (Zhong et al., 2007), response to pathogen infection (Xie et al., 1999; Saga et al., 2012) and adaption to the abiotic stress (Puranik et al., 2012; Wu et al., 2012; Nakashima et al., 2007; Tran et al., 2004; Shahnejat-Bushehri et al., 2012). Based on their response to abiotic stimuli, a set of NAC genes have been designated as Stress associated NAC (SNACs). These genes were used to develop transgenic plants. A transgenic rice with SNAC1 (ONAC045), OsNAC5 and OsNAC6 genes showed improved tolerance to drought and salt stresses (Hu et al., 2006; Zheng et al., 2009; Song et al., 2011); OsNAC10 and ONAC022 over-expressing rice plants showed improved drought tolerance (Jeong et al., 2010; Hong et al., 2016); NAC gene from finger millet (EcNAC1) conferred abiotic stress tolerance in tobacco (Ramegowda et al., 2012). Considering their significance in plant growth and development, whole genome search was done to identify NAC genes in many plants like Arabidopsis (117 NAC genes), rice (151), grape (79), citrus (26), poplar (163) soybean and tobacco (152), foxtail millet (147) and cotton (145) (Rushton et al., 2008; Hu et al., 2010; Nuruzzaman et al., 2010; Agri Gene 3 (2017) 1–11 Abbreviation: NAC, Nam Ataf Cuc2; TF, transcription factor; NAM, no apical meristem; ATAf, Arabidopsis transcription activator factor; CUC, cup shaped cotyledon; SNAC, stress associated NAC; Sc, sugar cane; Os, Oryza sativa; At, Arabidopsis thaliana; Zm, Zea mays; Sb, Sorghum bicolor. ⁎ Corresponding author at: Biotechnology, Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India. E-mail address: r.manimekalai@icar.gov.in (M. Ramaswamy). http://dx.doi.org/10.1016/j.aggene.2016.10.003 2352-2151/© 2016 Published by Elsevier Inc. Contents lists available at ScienceDirect Agri Gene journal homepage: www.elsevier.com/locate/aggene