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

Highlights

• Phylogenetic tree of NAC genes of sugarcane and its close relatives revealed distinct clades with orthologs and paralogs.

• Thirty paralogous ScNAC genes and 33 orthologous NAC genes between sugarcane and sorghum were identified.

• Identified stress associated sugarcane NAC: ScNAC34, ScNAC38, ScNAC40, ScNAC57, ScNAC63, ScNAC68, ScNAC83, ScNAC85 and ScNAC89.

• Stress associated ScNAC genes and their ortholog members are clustered together in the phylogenetic tree.

Abstract

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, comparative 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.

Introduction

NAC gene family is one of the largest and most important transcription factors in plants. The term NAC has been derived from three genes sharing common domain (Nac domain). These genes are; NAM (No apical 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 development (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, Puranik et al., 2013, Shang et al., 2013). Even though we have extensive literature on NAC genes in many crops, surprisingly there are no reports on NAC genes of sugarcane crop. In this report, we present the results of phylogenetic characterization of sugarcane NAC genes, their conserved motifs, comparative analysis of NAC genes from sugarcane and its closest relatives. Furthermore, in this manuscript we emphasize on NAC genes that are implicated in plant abiotic stresses.