Molecular Characterization and Expression Profiling of NAC Transcription Factors in Brachypodium distachyon L

Abstract

NAC (NAM, ATAF1/2, CUC2) transcription factors are involved in regulating plant developmental processes and response to environmental stresses. Brachypodium distachyon is an emerging model system for cereals, temperate grasses and biofuel crops. In this study, a comprehensive investigation of the molecular characterizations, phylogenetics and expression profiles under various abiotic stresses of the NAC gene family in Brachypodium distachyon was performed. In total, 118 BNAC genes in B. distachyon were identified, of which 22 (18.64%) were tandemly duplicated and segmentally duplicated, respectively. The Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC) algorithms showed that they were divided into two clades and fourteen subfamilies, supported by similar motif compositions within one subfamily. Some critical amino acids detected using DIVERGE v3.0 might contribute to functional divergence among subfamilies. The different exon-intron organizations among subfamilies revealed structural differentiation. Promoter sequence predictions showed that the BNAC genes were involved in various developmental processes and diverse stress responses. Three NAC domain-encoding genes (BNAC012, BNAC078 and BNAC108), orthologous of NAC1, were targeted by five miRNA164 (Bdi-miR164a-c, e, f), suggesting that they might function in lateral organ enlargement, floral development and the responses to abiotic stress. Eleven (~9.32%) BNAC proteins containing α-helical transmembrane motifs were identified. 23 representative BNAC genes were analyzed by quantitative real-time PCR, showing different expression patterns under various abiotic stresses, of which 18, 17 and 11 genes were up-regulated significantly under drought, H2O2 and salt stresses, respectively. Only four and two genes were up-regulated under cold and cadmium stresses, respectively. Dynamic transcriptional expression analysis revealed that six genes showed constitutive expression and period-specific expression. The current results provide novel insights into the structure and function of the plant NAC gene family.

Systematic Identification and Analysis of NAC Gene Family in Moso Bamboo (Phyllostachys edulis)

“…First, the latest data about Phyllostachys edulis including CDS (coding sequence), peptide sequences, genome sequence and scaffold location information were downloaded from the website (http://gigadb.org/dataset/view/tdsourcetag/s_pcqq_aiomsg/id/100498/File_sort/name/File_page/2). Then the NAC protein sequences from other species (Arabidopsis thaliana, Oryza sativa, Brachypodium distachyon, Sorghum bicolor and Zea mays) including 116 AtNACs [41], 143 OsNACs [42], 114 BNACs [43], 180 SbNACs [44], 144 ZmNACs [45] (some protein sequences were not found at https://phytozome.jgi.doe.gov/pz/portal.html) were used for blast ( Basic Local Alignment Search Tool) in moso bamboo latest peptide database with E value ≤1e-10 [46]. Next, the obtained results were veri ed to the existence of NAM domain (PF02365) in pfam website (http://pfam.xfam.org/search).…”

“…Then moso bamboo seedlings were cultivated for 8 weeks in 25±2 °C greenhouse photoperiod for 16 h light/8 h dark. And 200 mM NaCl [43], 100 μM methyl jasmonate (MeJA) [54] and 100 μM abscisic acid (ABA) [50] were sprayed on the leaves. For drought stress, 20% PEG6000 [44] were selected to irrigate the roots.…”

“…In addition, the majority of NAC genes in moso bamboo and other species contained two introns, indicating that the family was structurally conservative (Fig. 2) [43]. Strikingly, the members of subfamily F, PheNAC096/097and PheNAC095/096 were two pairs of paralogous genes, but the three members had different numbers of introns: PheNAC095-(1), PheNAC096-(8), PheNAC097-(0), indicating PheNAC095 and PheNAC097 might lose introns during evolution process.…”

Cloning, Characterization, and Expression Analysis of Eight Stress‐Related NAC Genes in Tartary Buckwheat

“…As studies have reported, there are interactions and crosstalk between stress and hormone signaling transduction Nakashima et al, 2012;Nuruzzaman et al, 2013). (Zhu et al, 2015), Populus trichocarpa L. (Hu et al, 2010), Setaria italica (L.) P. Beauv. Ectopic expression of ATAF1 can increase plant sensitivity to ABA, salt, and oxidative stresses and improve tolerance to drought in transgenic Arabidopsis (Wu et al, 2009).…”

“…Currently, stress-related NAC genes have also been reported from other plants, including Brachypodium distachyon (L.) P. Beauv. (Zhu et al, 2015), Populus trichocarpa L. (Hu et al, 2010), Setaria italica (L.) P. Beauv. (Puranik et al, 2013), and Miscanthus lutarioriparius Liu ex Chen & Renvoize ( Ji et al, 2014;Yang et al, 2015).…”