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Identification and Molecular Characterization of MYB Transcription Factor Superfamily in C4 Model Plant Foxtail Millet (Setaria italica L.)

Identification and Molecular Characterization of MYB Transcription Factor Superfamily in C4 Model Plant Foxtail Millet (Setaria italica L.)

  • Mehanathan Muthamilarasan, 
  • Rohit Khandelwal, 
  • Chandra Bhan Yadav, 
  • Venkata Suresh Bonthala, 
  • Yusuf Khan, 
  • Manoj Prasad
PLOS
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Abstract

MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I - X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli.

Introduction

In plants, transcription factors (TFs) play crucial role in regulating the gene expression and thereby guiding various biological processes including growth, development, cell division and response to stresses. Deciphering the molecular and physiological roles of these TFs has become hottest topic of research since understanding the control of gene expression would enable researchers to develop elite varieties of crop plants with desired agronomic traits which will ensure global food security in the scenario of climate change. Hence research on TFs had gained momentum and numerous TFs regulating vital biological processes in plants have been identified. MYB (myeloblastosis) TFs are omnipresent in eukaryotic systems and in plants was first identified in Zea mays involving the regulation of anthocyanin biosynthesis [1].

MYB proteins possess a highly conserved MYB DNA-binding domain throughout the eukaryotes at N-terminus and 1–4 imperfect repeats (R0, R1, R2, and R3) [2]. Each of these repeats contains 50–53 amino acids and encodes three α-helices, with second and third helices forming a helix–turn–helix (HTH) structure. Upon binding to DNA, HTH intercalates in the major groove [2], [3]. In addition, each MYB repeat comprises three regularly spaced tryptophan residues, which form a cluster in a hydrophobic core of the repeat and stabilize the structure of DNA-binding domain [4]. Contrarily, C-terminus is the activation domain and varies significantly between MYB proteins, which results in wide range of regulatory roles of MYB gene family [3], [5], [6].

There are numerous reports available demonstrating the role of MYB TFs in various plant processes such as secondary metabolism [7][10], hormone signal transduction [11], [12], environmental stresses [13][15], cell structuring and organ development [16][19]. The emergence of next-generation sequencing technologies and high-throughput analysis platforms had expedited genome sequencing projects in crop plants [20]. The availability of genome sequence information facilitated the crop research community to perform genome-wide analysis of TFs which would be more informative in conducting further research on functional characterization of candidate TFs. Of the various TFs, MYBs are most extensively studied in almost all land plants whose genome sequence is available [21][25], though there was no such genome-wide study on MYB TFs conducted in foxtail millet (Setaria italica L.).

Foxtail millet is a member of Poaceae family and it is the second most-widely cultivated millets, next to pearl millet (FAOSTAT 2012; http://faostat.fao.org/). Being a C4 panicoid crop, it is efficient in photosynthesis and better water use efficiency (WUE). Photosynthesis in C4 crops is more efficient than C3 plants even under high light intensity and high temperatures since phosphoenolpyruvate carboxylase (PEPC) helps in immediate uptake of carbon di oxide and delivering it to RuBisCO. The immediate quenching of carbon di oxide and delivery by PEPC does not require keeping stomata open for a long period and hence less water is lost by transpiration resulting in better WUE [26], [27]. Moreover, foxtail millet has been considered as a model crop for studying systems biology of biofuel crops due to its close phylogenetic relationships with several biofuel crops such as switchgrass (Panicum virgatum), napier grass (Pennisetum purpureum) and pearl millet (Pennisetum glaucum) [26], [27]. Hence considering its importance, BGI (Beijing Genomics Institute), China and the Joint Genome Institute (JGI) of Department of Energy, USA has sequenced the genome of two foxtail millet accessions [28], [29]. This motivated the present study, to perform (i) genome-wide identification of MYB TFs encoded in foxtail millet genome, (ii) protein and gene structure analysis using proteomic tools as well as phylogenetic analysis, (iii) promoter and miRNA analysis, (iv) in silico expression profiling using RNA-Seq data, (v) ortholog identification in related grass genomes, (vi) evolutionary analysis of orthologs and paralogs, and (vii) expression analysis of candidate MYB genes using qRT-PCR.

Materials and Methods

Identification, chromosomal location and gene duplication analysis of MYB proteins

The Hidden Markov Model (HMM) profile of MYB DNA-binding domain (PF00249) downloaded from Pfam v27.0 (http://pfam.sanger.ac.uk/family/PF00249) [30] was queried against Phytozome v9.1 (www.phytozome.net) of Setaria italica. All hits with expected values less than 1.0 were retrieved and compared with MYB protein dataset available in Foxtail millet Transcription Factor Database (http://59.163.192.91/FmTFDb/) [31]. In addition, S. italica MYB (SiMYB) proteins were examined using CDD search (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) for presence of one or more MYB DNA-binding domains. The chromosomal location and identification of alternate transcripts of SiMYBs were performed by executing BLASTP search against the foxtail millet protein sequences in Phytozome and redundant sequences with different identification numbers and same chromosome locus were discarded. Based on ascending order of chromosomal position from short arm telomere to long arm telomere, SiMYBs were annotated as SiMYB001 to SiMYB209 and physical map was constructed using MapChart v2.2 [32]. The map was manually inspected for identifying tandem duplications. Adjacent genes of same sub-family located within 10 predicted genes apart or within 30 kb of each-other are considered as tandem duplicated genes [33][36]. Segmental duplications were predicted using Multiple Collinearity Scan toolkit (MCScanX) [37] as described by Puranik et al. [35] and Mishra et al. [36].

Protein structure, gene organization and phylogenetic analysis

The presence of conserved domains in SiMYB proteins were analysed by employing hmmscan tool (http://hmmer.janelia.org/search/hmmscan). BioEdit tool (http://www.mbio.ncsu.edu/bioedit/bioedit.html) was used to perform multiple sequence alignment (MSA) of SiMYB amino acid sequences. The physicochemical properties of SiMYB proteins were then investigated using ExPASy ProtParam tool (http://web.expasy.org/protparam/). Gene Structure Display Server was used to identify the position of introns and exons in respective SiMYB genes (http://gsds.cbi.pku.edu.cn/) [38]. The SiMYB protein sequences were then imported into MEGA v6.06 [39] and MSA was performed using ClustalW with default parameters. The alignment file was used to construct neighbor-joining phylogenetic tree using a bootstrapping method with 1000 replicates.

Gene Ontology annotation, promoter analysis and prediction of miRNAs targeting SiMYBs

The amino acid sequences of SiMYB are loaded in Blast2GO suite [40] to perform BLASTP, against Oryza sativa protein sequences of NCBI, with default parameters. The hits were mapped to retrieve GO terms and annotation of GO terms associated with BLAST hits was executed. For promoter analysis, 2 kb upstream sequences of SiMYB genes were retrieved from Phytozome through in-house perl programming and cis-regulatory elements were identified using database of Plant Cis-acting Regulatory DNA Elements (PLACE) [41]. Moreover, Setaria italica miRNAs (Sit-miRs) targeting SiMYBs were predicted by aligning Sit-miRs [42], [43] with SiMYB transcript sequences using psRNATarget [44].

In silico expression profiling and marker localization

Setaria italica Illumina RNA-HiSeq reads for 4 tissues namely spica, stem, leaf and root were retrieved from European Nucleotide Archive [SRX128226 (spica); SRX128225 (stem); SRX128224 (leaf); SRX128223 (root)] [45]. The RNA-seq data was then filtered by NGS toolkit (http://59.163.192.90:8080/ngsqctoolkit/) [46] to remove low quality reads and mapped onto the gene sequences of S. italica using Bowtie2 [47]. The number of reads mapped was normalized by RPKM (reads per kilobase per million) method. The heat map showing tissue specific expression was generated on RPKM values for each gene in all the tissue samples using TIGR MultiExperiment Viewer (MeV4) software [48], [49]. The physical positions of DNA markers reported in foxtail millet [50] including simple sequence repeats (SSRs) [51], [52], EST-derived SSRs (eSSRs) [53] and intron length polymorphic markers (ILPs) [54], [55] were compared with the chromosomal location of SiMYB genes to identify the transcription factor gene-derived functional markers.

Identification of SiMYB orthologs in related grass genomes and evolutionary analysis of paralogs and orthologs

SiMYB protein sequences were BLASTP searched against the peptide sequences of sorghum, maize, rice and Brachypodium (http://www.gramene.org/; http://www.phytozome.net/) to predict the MYB orthologs in these grass species. A reciprocal BLAST (BLASTP) was also performed to ensure unique relationship between the orthologous genes and all hits with E-value≤1e-5 and at least 80% homology were considered significant. The orthologous relationships between foxtail millet and these grass species were then visualized using Circos v0.55 (http://circos.ca/). The synonymous (Ks) and non-synonymous (Ka) substitution rates were estimated for paralog and ortholog MYB gene pairs through CODEML program in PAML interface tool of PAL2NAL (http://www.bork.embl.de/pal2nal/) [56]. Time (million years ago, Mya) of duplication and divergence of SiMYB gene pairs were estimated using a synonymous mutation rate of λ substitutions per synonymous site per year, as T = Ks/2λ, where, λ = 6.5×10−9 [35], [57], [58], [59].

Plant materials and treatments

A salt and dehydration tolerant foxtail millet cultivar ‘Prasad’ [60], [61] was chosen for analysing the expression pattern of candidate SiMYBs. The seedlings were grown in a plant growth chamber (PGC-6L; Percival Scientific Inc., USA) for 21 d after germination at 28±1°C day/23±1°C night/70±5% relative humidity with a photoperiod of 14 h and a photosynthetic photon flux density of 500 µmol m−2 s−1. The plants were watered daily with one-third strength Hoagland's solution [62]. For stress and hormone treatments, 21-day-old seedlings were individually exposed to 250 mM NaCl (salinity), 20% PEG 6000 (dehydration), 100 µM abscisic acid (ABA), 100 µM methyl jasmonate (MJ) and 100 µM salicylic acid (SA) for 1 h (early) and 24 h (late) following previous reports [35], [61], [63]. After respective treatment, whole seedlings are immediately frozen in liquid nitrogen and stored at −80°C for RNA isolation. Untreated plants were maintained as control. The above experiments were repeated thrice to ensure precision and reproducibility.

RNA isolation and quantitative real-time PCR analysis

Total RNA was isolated by following the method described by Longeman et al. [64] and treated with RNase-free DNase I (50 U/µl; Fermentas, USA). Its quality and purity was ensured using NanoDrop Spectrophotometer (Thermo Fisher Scientific, USA) [OD260: OD280 nm absorption ratio (1.8–2.0)] and integrity of RNA was checked by resolving on 1.2% agarose gel containing 18% formaldehyde. An amount of ∼1 µg total RNA was reverse transcribed to first strand cDNA using random primers by Thermo Scientific Verso cDNA kit (Thermo Fisher Scientific, USA) following manufacturer's instructions. The qRT-PCR primers were designed using GenScript Real-time PCR Primer Design tool (https://www.genscript.com/ssl-bin/app/primer) (Table S1). qRT-PCR analysis was performed in three technical replicates for each biological duplicate by StepOne Real-Time PCR Systems (Applied Biosystems, USA). The PCR mixtures and reactions were used as described previously by Kumar et al. [65] Melting curve analysis (60 to 95°C after 40 cycles) and agarose gel electrophoresis were performed to check amplification specificity. A constitutive Act2 gene-based primer was used as endogenous control [65]. The amount of transcripts accumulated for SiMYB genes normalized to the internal control Act2 were analysed using 2−ΔΔCt method cDNA synthesis [65]. The PCR efficiency was calculated as: Efficiency = 10(−1/slope)−1 by the default software (Applied Biosystems).

Homology modeling and active site prediction

SiMYB protein sequences were searched against Protein Data Bank (PDB) (http://www.rcsb.org/pdb/) for predicting the best template with homologous amino acid sequence and known structure. The result was then imported in Phyre2 server (Protein Homology/AnalogY Recognition Engine; http://www.sbg.bio.ic.ac.uk/phyre2) for predicting three-dimensional structures of proteins by homology modeling under ‘normal’ mode [66]. Active sites were precited using COACH server (http://zhanglab.ccmb.med.umich.edu/COACH/) and highlighted using UCSF Chimera 1.8.

Results and Discussion

Identification of SiMYB genes

The availability of foxtail millet whole genome sequence [28], [29] facilitated genome wide identification of MYB transcription factor (TF) gene family. The HMM search showed the presence of 229 MYB genes in foxtail millet genome (Table S2). The result was then confirmed by comparing the data with Foxtail millet Transcription Factor Database (FmTFDb; http://59.163.192.91/FmTFDb/) [31]. Further, all 229 SiMYB genes were BLAST searched against foxtail millet genome in Phytozome to identify alternate transcripts and chromosomal location. The results showed that 209 SiMYBs were primary transcripts and 20 were alternate transcripts. SiMYB017 had a maximum of three alternate transcripts, whereas SiMYB080, SiMYB137, SiMYB143 and SiMYB185 have two splice variants. Thirteen SiMYBs were evidenced to have one splice variant each.

The 209 SiMYB genes reported in the present study is higher than the numbers reported in Arabidopsis (197) [67], grape (118) [68] and Populus (192) [69]. On contrary, this number is lesser than soybean (244) [23] and apple (229) [70] (Figure S1). Among sequenced grass genomes, foxtail millet was evidenced to encode for a highest number of MYB TFs. Its closest relative sorghum has 100 MYB genes, whereas maize, rice and Brachypodium has 132, 155 and 98 MYB genes, respectively (http://planttfdb.cbi.pku.edu.cn/; Figure S1). Of note, further experimentations are requisite to identify the pseudogenes among the 209 SiMYBs.

SiMYBs location and duplication in foxtail millet genome

All the 209 SiMYB genes were physically mapped onto nine chromosomes of foxtail millet (Figure 1). The map revealed an uneven distribution of SiMYB genes in foxtail millet genome (Table S2). Highest number of SiMYB genes were observed in chromosome 5 (39; ∼19%) and lowest in chromosome 8 (6; ∼3%), with a density of 0.8 and 0.1 MYB genes/Mb, respectively. The distribution pattern of SiMYBs on individual chromosomes also revealed certain physical regions with a relatively higher accumulation of gene clusters. For instance, SiMYBs located on chromosomes 1, 3, 4, 5, 6 and 9 appear to be clustered at both upper end and lower end of the arms. Moreover, examination of gene duplication showed that SiMYB genes underwent both tandem and segmental duplications (Figure 1). Twelve gene-pairs were evidenced to be segmentally duplicated, whereas 15 genes were tandemly duplicated.

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Figure 1. Physical map of 209 SiMYB genes.

SiMYB genes were plotted onto nine chromosomes of foxtail millet. The numbers at left indicates the position of SiMYB genes, and the names of the respective genes are given in right. The ‘MYB-Related’ are given in black, ‘MYB-R2R3’ are in blue and ‘MYB-R1R2R3’ are in red. The SiMYB genes used for expression analysis through qRT-PCR are underlined. Segmentally duplicated gene-pairs are highlighted with different colours. Tandemly duplicated gene-pairs are enclosed within red boxes.

https://doi.org/10.1371/journal.pone.0109920.g001

Structural classification of SiMYB proteins

The CDD search demonstrated the presence of conserved motifs in SiMYB proteins (Figure S2). It also showed the presence of more than one MYB repeats in some of these proteins along with the presence of additional domains. The hmmscan analysis provided comprehensive information on functional domains present in SiMYB proteins (Table S3). Based on the presence of one, two and three MYB repeats, the SiMYBs are classified into ‘MYB-related’, ‘MYB-R2R3’ and ‘MYB-R1R2R3’ (Table S2). The multiple sequence alignment of other three types of SiMYBs confirmed the presence of MYB repeats in the protein sequences (Figure S3S5). Of the three types, ‘MYB-R2R3’ genes were found to be in maximum (114; ∼55%) followed by ‘MYB-related’ (90; ∼43%). Only 5 ‘MYB-R1R2R3’ were evidenced in foxtail millet distributed one MYB-R1R2R3 encoding gene each in chromosome 1 to 5 (Figs. 1, 2). The predominance of ‘MYB-R2R3’ type SiMYBs suggest that they could have been evolved from MYB-R1R2R3 gene progenitor through loss of R1 repeat or from a MYB-R1 gene through duplication of R1 repeat [71], [72]. Interestingly, no ‘Atypical MYB’ was identified in the foxtail millet, though one ‘Atypical MYB’ was reported in rice, two each in Arabidopsis and soybean [23], [67]. Among ‘MYB-R2R3’ and ‘MYB-related’ genes, highest numbers were found to be encoded in chromosome 5 (19 each). The lowest number of these genes are in chromosome 8 (5; ∼4% and 1; ∼1%, respectively) (Figs. 1, 2).

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Figure 2. Chromosome-wise distribution of SiMYB genes.

The distribution of three different SiMYB genes on individual chromosomes is shown.

https://doi.org/10.1371/journal.pone.0109920.g002

Further, hmmscan analysis also revealed the presence of specific, functionally important domains present in C-terminal regions outside MYB domain which are involved in transcriptional activity and protein-protein interactions (Table S3). SiMYB003, SiMYB094, SiMYB160 and SiMYB185 possess SWIRM domain. It is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn-helix motif and binds to DNA [73]. ‘Response_reg’ is ‘response regulator receiver domain’, which was first identified to receive signal from the sensor partner in bacterial two-component systems. SiMYB004, SiMYB024, SiMYB082, SiMYB091, SiMYB093, SiMYB137, SiMYB193 and SiMYB207 have this domain. It is usually found at N-terminal to a DNA binding effector domain and its role in plant systems remain elusive [74]. The domain ‘P_C’ in SiMYB205 denotes ‘P protein C-terminus’, which represents C-terminus of plant P proteins. The maize P gene is a transcriptional regulator of genes encoding enzymes for flavonoid biosynthesis in the pathway leading to production of a red phlobaphene pigment [75] and P proteins are homologous to DNA-binding domain of MYB-like transcription factors [76]. The ‘ZZ’ domain is ZZ type-Zinc finger whose binding to DNA is not yet identified [77]. This domain is present in SiMYB094, SiMYB184 and SiMYB185. It has 4–6 cysteine residues in its sequence, which are responsible for coordinating zinc ions and to reinforce the structure [78]. SiMYB153 was evidenced to have ‘Bromodomain’, which is reported to recognize acetylated lysine residues. This recognition is prerequisite for protein-histone association and chromatin remodelling [79]. The domain ‘DUF3651’ is present in SiMYB055 and SiMYB106, which denotes ‘Domain of Unknown Function’. The ‘Linker_histone’ present in SiMYB110, SiMYB119, SiMYB127 and SiMYB188, which is an essential component of chromatin structure [80].

Except for the presence of conserved MYB domain, SiMYBs varied notably in size, sequence, intron-exon numbers and distribution and its physicochemical properties (Table S2). Gene structure analysis showed that 10 SiMYB were intron-less while SiMYB026 and SiMYB184 have maximum of 11 introns (Figure S6). The longest gene was SiMYB094 with 8194 bases and the shortest was SiMYB186 (348 bases). The longest protein sequence was SiMYB053 (1741 amino acids) and the least was SiMYB194 (98 amino acids) (Table S2). The enormous diversity with respect to MYB gene and proteins observed in foxtail millet was not reported in any other crop species [21][25], and this shows the presence of putative novel variants.

Phylogenetic classification of SiMYB proteins

The phylogenetic tree constructed using neighbour-joining (NJ) method for all 209 SiMYB proteins conformed to the phylogenetic classification enlisted in FmTFDb (Figure 3). The internal branches were detected to have high bootstrap values and this lead to the derivation of statistically reliable pairs of possible homologous proteins possessing similar functions from a common ancestor. Based on topology and clade support values, the phylogenetic tree was divided into ten clades (I to X) (Figure 3). Although SiMYB proteins tended to cluster together in the tree with respect to their type and they were not equally distributed in the clades which may be due to the occurrence of duplication and divergence of SiMYB genes (Figure 3).

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Figure 3. Phylogenetic relationships of foxtail millet MYB transcription factors.

The unrooted phylogenetic tree was constructed by neighbor-joining method with 1000 bootstrap replicates. The bootstrap values are shown at the nodes. The tree was divided into ten phylogenetic cluster designated as I to X.

https://doi.org/10.1371/journal.pone.0109920.g003

Gene Ontology annotation

Gene Ontology (GO) annotation for all 209 SiMYB proteins was performed using Blast2GO. The SiMYB protein sequences were BLAST searched against Oryza sativa protein database and its biological processes, molecular functions and cellular components were identified (Figure 4). The results indicate that SiMYB proteins participate in diverse biological and molecular functions in the cell (Table S4). Noteworthy, predominant of SiMYBs were predicted to function in regulation of transcription in a DNA-dependent manner, followed by playing pivotal role in trichome differentiation and androecium development. SiMYBs are reported to least participate in breaking seed dormancy (Figure 4). The biological function analysis also revealed that 68 (32.5%) SiMYB proteins function in response to stress (Table S4). The molecular role showed that most of SiMYBs have function in nucleic acid binding followed by cation binding. Cellular component data predicted that SiMYBs are nuclear localized. In addition, SiMYB proteins were also indicated to localize in plastids and mitochondria (Figure 4). In addition, Blast2GO was performed to correlate the domain composition of families/sub-families with functional classes, but no correlation was observed.

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Figure 4. Gene Ontology distribution for SiMYB proteins.

Blast2GO program defines the gene ontology under three categories. (A) biological processes, (B) molecular functions and (C) cellular component.

https://doi.org/10.1371/journal.pone.0109920.g004

Cis-acting elements and SiMYB targeting miRNAs

The promoter analysis identified ∼300 diverse cis-acting elements upstream of SiMYB genes (Table S5). Of these, ARR1AT, CAATBOX1, CACTFTPPCA1, DOFCOREZM, EBOXBNNAPA, GATABOX, GT1CONSENSUS, GTGANTG10, MYCCONSENSUSAT, POLLEN1LELAT52, WBOXNTERF3 and WRKY71OS were present in all 209 SiMYB genes. ARR1AT (NGATT) is a cytokinin response regulator binding motif [81] and CAATBOX1 (CAAT) are reported to regulate flowering [82]. CACTFTPPCA1 (CACGTG) is responsible for mesophyll-specific gene expression of C4 phosphoenolpyruvate carboxylase gene in C4 plants [83] and DOFCOREZM (AAAG) is the binding cite of Dof transcription factors [84]. EBOXBNNAPA (CANNTG) is E-box sequence responsible for light responsiveness and is regulated by bHLH and MYB-transcription factor in directing tissue-specific expression [13]. GATABOX (GATA) is the binding site for transcription factors with a zinc finger motif [85], GT1CONSENSUS (GRWAAW) recognizes GT-1 proteins which have tri-helix DNA-binding domains [86] and GTGANTG10 (GTGA) is a pollen-specific cis-elements [87]. MYCCONSENSUSAT (CANNTG) is a MYC recognition site which regulates transcription of genes under cold conditions by a MYC-like bHLH transcriptional activator [88], POLLEN1LELAT52 (AGAAA) is a regulatory element responsible for pollen-specific activation of gene expression [89], WBOXNTERF3 (TGACY) is a W-box promoter motif functioning in response to wound signal [90] and WRKY71OS (TGAC) is a binding site of rice WRKY71, a transcriptional repressor of gibberellin signaling pathway [91]. In addition to these, some cis-elements were present unique to specific SiMYBs such as AAGACGTAGATACL12 in SiMYB167, ABADESI1 in SiMYB025, ABADESI2 in SiMYB110, ABRE3HVA22 in SiMYB158 and ABREDISTBBNNAPA in SiMYB122. Further, Setaria italica miRNAs (Sit-miRs) targeting the SiMYB transcripts for post-transcriptional gene regulation were also identified. Three Sit-miRs namely Sit-miR5568.58, Sit-miR2118d and Sit-miR159a were evidenced to target SiMYB026, SiMYB028, SiMYB029, SiMYB130 and SiMYB190 (Table 1). This data would assist in deciphering post-transcriptional control of gene regulation during physiological and stress-induced cellular responses.

Heat map analysis and identification of transcription factor-derived markers

The publicly available Illumina RNA-Seq data for four tissues of foxtail millet root, leaf, stem and spica were used to analyse the expression pattern of SiMYB genes. The heat map showed differential expression of SiMYBs across the tissues (Figure 5). Predominant of MYB genes including SiMYB003, SiMYB004, SiMYB005, SiMYB017, SiMYB025, SiMYB051, SiMYB064, SiMYB080, SiMYB089, SiMYB090, SiMYB0100 were predicted to be highly expressed in all the tissues. Interestingly, tissue-specific higher expression was also noted. SiMYB007 and SiMYB087 were highly expressed in leaf, while SiMYB192 showed higher expression in root (Figure 5). This expression profiling would facilitate combinatorial usage of SiMYBs in transcriptional regulation of different tissues, whereas ubiquitously expressed SiMYBs might regulate the transcription of a broad set of genes. Further, this heat map data also enables selection and designing of studies to impart stress tolerance in both foxtail millet and related crop species.

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Figure 5. Heat map representation of SiMYB genes in four tissues.

The Illumina RNA-seq data were re-analyzed and heat map was generated. Bar at the top represents log2 transformed values, thereby values 0.0, 2.0 and 8.0 represent low, intermediate and high expression, respectively.

https://doi.org/10.1371/journal.pone.0109920.g005

In addition, molecular markers present in SiMYBs were also identified. Seventy three SiMYB genes (∼35%) were evidenced to possess DNA markers (Table S6). Of the various types of markers reported in foxtail millet, presence of microsatellites (SSRs and eSSRs) in SiMYBs were found predominant (∼90%) followed by ILP markers (∼10%). Among the SSRs (63), tri-nucleotide repeats were maximum (41) followed by di-nucleotide repeats (20). Only two eSSRs namely SieSSR302 and SieSSR70 were found to be present in SiMYB030 and SiMYB094, respectively, and both the markers were of tri-nucleotide repeat type. SSRs SiGMS12780 and SiGMS8287 were a tetra- and hexa-nucleotide repeats, evidenced to be present in SiMYB179 and SiMYB125, respectively (Table S6). The functional relevance of these informative genic markers needs to be demonstrated by integrating agronomic trait association analysis with genetic mapping, differential expression profiling, protein modelling and haplotype gene evolution study in relation to MYB genes.

SiMYB orthologs in sorghum, maize, rice and Brachypodium

Of the 209 SiMYB genes, 72 (∼34%) showed significant orthologous relationships with sorghum, 55 (∼26%) with maize, 23 (∼11%) with rice and 13 (∼6%) with Brachypodium (Figure 6; Tables S7S10). Foxtail millet chromosome 5 showed highest synteny with sorghum chromosome 3 (14; ∼19%), and maize chromosomes 3 and 8 (11; 20%). Chromosome 3 of foxtail millet has highest orthologous pairs with rice chromosomes 4, 5 and 12 (∼22%), and Brachypodium chromosomes 2, 4 and 5 (∼38%). Except the presence of conserved nucleotide and amino acid sequences of MYB domain between foxtail millet-rice and foxtail millet-Brachypodium, the regions other than the MYB domain were highly diverse. The degree of decrease in orthologous relationships among foxtail millet-sorghum, -maize, -rice and Brachypodium is due to genetic relatedness of these genomes. Foxtail millet along with sorghum and maize belong to Panicoideae, whereas rice and Brachypodium belong to Ehrhartoideae and Pooideae, respectively. This pattern of decreasing synteny was also observed in the comparative mapping of NAC TFs [35], WD40 genes [36], Dicer-like, Argonaute, RNA-dependent RNA polymerase genes [92], and C2H2-type zinc finger TFs [59]. This comparative map would enable the researchers to select candidate MYB genes from foxtail millet and utilize them in genetic enhancement of related grass family members.

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Figure 6. Comparative physical mapping revealed high degree of orthologous relationships of SiMYB genes located on nine chromosomes of foxtail millet.

(A) Sit (foxtail millet) – Sbi (sorghum), (B) SitZma (maize), (C) SitOsa (rice), and (D) SitBdi (Brachypodium).

https://doi.org/10.1371/journal.pone.0109920.g006

Evolutionary aspects of duplication and divergence

The ratios of non-synonymous (Ka) versus synonymous (Ks) substitution rate (Ka/Ks) were estimated for duplicated and orthologous gene-pairs of SiMYB. The ratios of Ka/Ks for segmentally and tandemly duplicated gene-pairs ranged from 0.02 to 0.1 and 0.07 to 0.1, respectively (Tables S11S12). The estimated Ka/Ks was <1, and this justified that the duplicated SiMYB genes were under strong purifying selection pressure. This is in agreement with previous genome-wide reports on NAC TFs by Puranik et al. [35], WD40 gene family by Mishra et al. [36], and C2H2-type zinc finger TFs by Muthamilarasan [59]. In addition, it was also estimated that the duplication event of these segmentally and tandemly duplicated genes occurred ∼33 Mya (Figure 7). Although further experimentations are necessary to validate this, the present study suggests that these duplication events must be specific to Setaria since divergence of sorghum and maize had occurred ∼13 Mya [28], [29].

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Figure 7. Time of duplication and divergence (MYA) based on synonymous substitution rate (Ks) estimated using duplicated SiMYB gene-pairs of foxtail millet and orthologous MYB gene pairs between foxtail millet- sorghum, -maize, -rice and Brachypodium.

https://doi.org/10.1371/journal.pone.0109920.g007

Among orthologous gene-pairs of SiMYB, average Ka/Ks value was maximum between foxtail millet and Brachypodium followed by foxtail millet and rice (Figure 7). The Ka/Ks was minimum for foxtail millet-sorghum gene-pairs. The relatively higher rate of synonymous substitution between Brachypodium and foxtail millet MYB genes suggested their earlier divergence around 42 Mya. The evolutionary analysis also predicts the divergence time of foxtail millet-rice as ∼39 MYA, foxtail millet-maize as ∼29 MYA and foxtail millet-sorghum as ∼27 MYA (Figure 7). These Ka/Ks dating data along with comparative map would assist in understanding the evolution of MYB genes in grasses genomes.

Expression pattern of SiMYBs under abiotic stress and hormone treatments

To study the expression patterns of identified SiMYBs, 11 candidate SiMYB genes were chosen representing all the nine chromosomes of foxtail millet and all the 10 clades of phylogenetic tree. The relative transcript abundance of these candidate MYBs at both early (1 h) and late (24 h) duration of abiotic stresses (salinity and dehydration), and hormone treatments (ABA, MJ, SA) were studied using qRT-PCR (Figure 8). During early phase of salinity stress SiMYB003, SiMYB100, SiMYB124 and SiMYB174 were highly up-regulated whereas SiMYB041, SiMYB074, SiMYB126, SiMYB150 and SiMYB202 were down-regulated. Though SiMYB100 and SiMYB174 showed significant up-regulation during early hours of salinity stress, a drastic down-regulation was observed at late phase. SiMYB150 showed ∼2 fold higher expression during late phase of salinity stress. In course of dehydration stress, up-regulation during early phase was evidenced in SiMYB074, SiMYB100, SiMYB174 and SiMYB202. SiMYB124 showed higher expression at both early and late phases. A drastic up-regulation of SiMYB genes at 24 h after dehydrations stress was noticed in SiMYB126, SiMYB110 and SiMYB184.

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Figure 8. The relative expression ratio of 11 candidate SiMYB genes analysed using qRT-PCR under salinity stress, dehydration stress and hormone treatments for 1 h (early) and 24 h (late).

The relative expression ratio of each gene was calculated relative to its expression in control sample (0 h). Act2 was used as an internal control to normalize the data. Error bars representing standard deviation were calculated based on three technical replicates for each biological duplicate. ABA - abscisic acid, MJ - methyl jasmonate, SA - salicylic acid.

https://doi.org/10.1371/journal.pone.0109920.g008

During hormone treatments, SiMYB126, SiMYB150 and SiMYB177 were down-regulated in all the treatments and time points, except a considerable higher expression of SiMYB126 and SiMYB177 at 24 h post ABA treatment. SiMYB003 was down-regulated at both the phases of ABA treatment, while significant up-regulation at 24 h post ABA application was observed in SiMYB184 and SiMYB202. The genes SiMYB003, SiMYB100 and SiMYB184 were up-regulated during early phase of MJ treatment, whereas up-regulation was observed at late phase in SiMYB074 and SiMYB202. Up-regulation of SiMYB100 and SiMYB184 was evidenced in early phase of SA treatment. After 24 h, SiMYB003 and SiMYB202 showed higher expression.

Since foxtail millet is well known for its adaptability to abiotic stresses such as dehydration and salinity [60][62], deciphering the role of MYB TFs will provide novel insights into the stress tolerance mechanism of this model crop. This preliminary study on expression profiling of candidate SiMYB genes in response to different stress and hormone treatments would serve as a foundation for downstream characterization of these TFs.

Homology modelling of SiMYB proteins

Three dimensional protein models were constructed for all 209 SiMYBs and of note, the proteins were modelled at 90% confidence (Table S13). Further, its potential active sites were also identified (Figure S7). As mentioned earlier, the SiMYBs were classified into ‘MYB-related’, ‘MYB-R2R3’ and ‘MYB-R1R2R3’ based on the presence of one, two and three MYB repeats in the N-terminus. The homology modelling showed that each MYB repeat comprised of 52 amino acids and encoded three α-helices, with the second and third helices forming a helix-turn-helix (HTH) structure. Further, it included three regularly spaced tryptophan residues, forming a hydrophobic core in the three dimensional HTH structure (Figure S7). The third helix of each repeat formed ‘recognition helix’, which was reported to interact with DNA and intercalate in the major groove [6]. Contrarily, the C-terminus varied considerably between SiMYB proteins and this could be responsible for the wide range of regulatory roles of SiMYB gene family. This preliminary data would provide a base for further molecular structure analyses and interaction studies of SiMYB proteins.

In summary, the present study identified 209 MYB proteins in model crop foxtail millet and physically mapped them onto the genome. The protein structure and gene organization of individual SiMYBs were analysed and a phylogenetic tree was constructed. The domain analysis showed the presence of diverse protein domains in MYB proteins and the multiple sequence alignment revealed the conserved sequences in these domains. In addition, DNA markers present in SiMYB genes were also investigated. Candidate SiMYBs were chosen for expression profiling through qRT-PCR and the analysis showed the role of these genes in response to abiotic stresses and hormone treatments. The present study is the first report on genome-wide identification, characterization and expression profiling of MYB transcription factors in foxtail millet and promisingly, the data obtained from this study would contribute to a better understanding of the complexity of MYB TFs in plants and provide a useful reference for further functional analysis of MAPK genes in foxtail millet and related grasses.

Supporting Information

Figure S1.

Phylogenetic relationships between all the sequenced plant species. The total number of MYB proteins found in each genome is indicated on the right. The data was retrieved from PlantTFDB (http://planttfdb.cbi.pku.edu.cn/). The data of foxtail millet (Setaria italica) excludes alternate transcripts.

https://doi.org/10.1371/journal.pone.0109920.s001

(PDF)

Figure S2.

Conserved domains in SiMYB proteins, identified using CDD database.

https://doi.org/10.1371/journal.pone.0109920.s002

(PDF)

Figure S3.

The multiple sequence alignment of ‘MYB-related’ proteins.

https://doi.org/10.1371/journal.pone.0109920.s003

(PDF)

Figure S4.

The multiple sequence alignment of ‘MYB-R2R3’ proteins.

https://doi.org/10.1371/journal.pone.0109920.s004

(PDF)

Figure S5.

The multiple sequence alignment of ‘MYB-R1R2R3’ proteins.

https://doi.org/10.1371/journal.pone.0109920.s005

(PDF)

Figure S6.

Gene structures of SiMYB proteins. Exons and introns are represented by green boxes and black lines, respectively.

https://doi.org/10.1371/journal.pone.0109920.s006

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Figure S7.

Predicated three dimensional structures of all the 209 SiMYB proteins.

https://doi.org/10.1371/journal.pone.0109920.s007

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Table S1.

Details of primers used for quantitative real-time PCR.

https://doi.org/10.1371/journal.pone.0109920.s008

(DOC)

Table S2.

Characteristic features of 209 MYB Transcription factor gene family members identified in Setaria italica.

https://doi.org/10.1371/journal.pone.0109920.s009

(XLS)

Table S3.

Summary of functional domains present in the 209 SiMYB proteins.

https://doi.org/10.1371/journal.pone.0109920.s010

(XLS)

Table S4.

Blast2GO annotation details of SiMYB protein sequences.

https://doi.org/10.1371/journal.pone.0109920.s011

(XLS)

Table S5.

Characteristics of the promoter region of SiMYB genes.

https://doi.org/10.1371/journal.pone.0109920.s012

(XLS)

Table S6.

Details of DNA markers present in SiMYB genes.

https://doi.org/10.1371/journal.pone.0109920.s013

(XLS)

Table S7.

The Ka/Ks ratio, estimated divergence time and percentage identity for orthologous SiMYB proteins between foxtail millet and sorghum.

https://doi.org/10.1371/journal.pone.0109920.s014

(XLS)

Table S8.

The Ka/Ks ratio, estimated divergence time and percentage identity for orthologous SiMYB proteins between foxtail millet and maize.

https://doi.org/10.1371/journal.pone.0109920.s015

(XLS)

Table S9.

The Ka/Ks ratio, estimated divergence time and percentage identity for orthologous SiMYB proteins between foxtail millet and rice.

https://doi.org/10.1371/journal.pone.0109920.s016

(XLS)

Table S10.

The Ka/Ks ratio, estimated divergence time and percentage identity for orthologous SiMYB proteins between foxtail millet and Brachypodium.

https://doi.org/10.1371/journal.pone.0109920.s017

(XLS)

Table S11.

The Ka/Ks ratios and estimated divergence time for segmentally duplicated SiMYB genes.

https://doi.org/10.1371/journal.pone.0109920.s018

(DOC)

Table S12.

The Ka/Ks ratios and estimated divergence time for tandemly duplicated SiMYB genes.

https://doi.org/10.1371/journal.pone.0109920.s019

(DOC)

Table S13.

List of templates used in homology modelling of 209 SiMYB proteins.

https://doi.org/10.1371/journal.pone.0109920.s020

(XLS)

Acknowledgments

MM acknowledges the award of Junior Research Fellowship from University Grants Commission, New Delhi, India. Assistance from Ms Jananee Jaishankar and Mr Subodh Verma, NIPGR is greatly appreciated.

Author Contributions

Conceived and designed the experiments: MP. Performed the experiments: MM RK CBY VSB YK. Analyzed the data: MP MM. Wrote the paper: MM MP.

References

  1. 1. Paz-Ares J, Ghosal D, Wienand U, Peterson PA, Saedler H (1987) The regulatory c1 locus of Zea mays encodes a protein with homology to myb proto-oncogene products and with structural similarities to transcriptional activators. EMBO J 6: 3553–3558.
  2. 2. Lipsick JS (1996) One billion years of Myb. Oncogene 13: 223–235.
  3. 3. Stracke R, Werber M, Weisshaar B (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Bio l4: 447–456.
  4. 4. Ogata K, Morikawa S, Nakamura H, Hojo H, Yoshimura S, et al. (1995) Comparison of the free and DNA-complexed forms of the DNA–binding domain from c-Myb. Nat Struct Biol 2: 309–320.
  5. 5. Jin H, Martin C (1999) Multifunctionality and diversity within the plant MYB-gene family. Plant Mol Biol 41: 577–585.
  6. 6. Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, et al. (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci 15: 573–581.
  7. 7. Goicoechea M, Lacombe E, Legay S, Mihaljevic S, Rech P, et al. (2005) EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis. Plant J 43: 553–567.
  8. 8. Mehrtens F, Kranz H, Bednarek P, Weisshaar B (2005) The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis. Plant Physiol 138: 1083–1096.
  9. 9. Bedon F, Grima–Pettenati J, Mackay J (2007) Conifer R2R3–MYB transcription factors: sequence analyses and gene expression in wood-forming tissues of white spruce (Picea glauca). BMC Plant Biol 7: 17.
  10. 10. Stracke R, Ishihara H, Huep G, Barsch A, Mehrtens F, et al. (2007) Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. Plant J 50: 660–677.
  11. 11. Gocal GF, Poole AT, Gubler F, Watts RJ, Blundell C, et al. (1999) Long-day up-regulation of a GAMYB gene during Lolium temulentum inflorescence formation. Plant Physiol 119: 1271–1278.
  12. 12. Abe H, Urao T, Ito T, Seki M, Shinozaki K, et al. (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15: 63–78.
  13. 13. Hartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B (2005) Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes. Plant Mol Biol 57: 155–171.
  14. 14. Jung C, Seo JS, Han SW, Koo YJ, Kim CH, et al. (2008) Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis. Plant Physiol 146: 623–635.
  15. 15. Adler G, Blumwald E, Bar–Zvi D (2010) The sugar beet gene encoding the sodium/proton exchanger 1 (BvNHX1) is regulated by a MYB transcription factor. Planta 232: 187–195.
  16. 16. Higginson T, Li SF, Parish RW (2003) AtMYB103 regulates tapetum and trichome development in Arabidopsis thaliana. Plant J 35: 177–192.
  17. 17. Perez-Rodriguez M, Jaffe FW, Butelli E, Glover BJ, Martin C (2005) Development of three different cell types is associated with the activity of a specific MYB transcription factor in the ventral petal of Antirrhinum majus flowers. Development 132: 359–370.
  18. 18. Baumann K, Perez–Rodriguez M, Bradley D, Venail J, Bailey P, et al. (2007) Control of cell and petal morphogenesis by R2R3 MYB transcription factors. Development 134: 1691–1701.
  19. 19. Pattanaik S, Kong Q, Zaitlin D, Werkman JR, Xie CH, et al. (2010) Isolation and functional characterization of a floral tissue-specific R2R3 MYB regulator from tobacco. Planta 231: 1061–1076.
  20. 20. Muthamilarasan M, Theriappan P, Prasad M (2013) Recent advances in crop genomics for ensuring food security. Curr Sci 105: 155–158.
  21. 21. Dias AP, Braun EL, McMullen MD, Grotewold E (2003) Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication. Plant Physiol 131: 610–620.
  22. 22. Li Q, Zhang C, Li J, Wang L, Ren Z (2012) Genome-wide identification and characterization of R2R3MYB family in Cucumis sativus. PLoS ONE 7: e47576.
  23. 23. Du H, Yang SS, Feng BR, Liu L, Tang YX (2012) Genome-wide analysis of the MYB transcription factor superfamily in soybean. BMC Plant Biol 12: 106.
  24. 24. Du H, Feng BR, Yang SS, Huang YB, Tang YX (2012) The R2R3-MYB transcription factor gene family in maize. PLoS ONE 7: e37463.
  25. 25. Du H, Wang YB, Xie Y, Liang Z, Jiang SJ, et al. (2013) Genome-wide identification and evolutionary and expression analyses of MYB-related genes in land plants. DNA Res 20: 437–448.
  26. 26. Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet: A sequence-driven grass model system. Plant Physiol 149: 137–141.
  27. 27. Lata C, Gupta S, Prasad M (2013) Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses. Crit Rev Biotechnol 33: 328–343.
  28. 28. Zhang G, Liu X, Quan Z, Cheng S, Xu X, et al. (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotech 30: 549–554.
  29. 29. Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, et al. (2012) Reference genome sequence of the model plant Setaria. Nature Biotechnol 30: 555–561.
  30. 30. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, et al. (2014) The Pfam protein families database. Nucleic Acids Res 42: D222–D230.
  31. 31. Bonthala VS, Muthamilarasan M, Roy R, Prasad M (2014) FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets. Mol Biol Rep DOI:https://doi.org/ 10.1007/s11033-014-3574-y.
  32. 32. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77–78.
  33. 33. Du D, Zhang Q, Cheng T, Pan H, Yang W, et al. (2012) Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume. Mol Biol Rep 40: 1937–1946.
  34. 34. Shiu S–H, Bleecker AB (2003) Expansion of the Receptor-Like Kinase/Pelle Gene Family and Receptor-Like Proteins in Arabidopsis. Plant Physiol 132: 530–543.
  35. 35. Puranik S, Sahu PP, Mandal SN, B VS, Parida SK, et al. (2013) Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.). PLoS ONE 8: e64594.
  36. 36. Mishra AK, Muthamilarasan M, Khan Y, Parida SK, Prasad M (2014) Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet (Setaria italica L.). PLoS ONE 9: e86852.
  37. 37. Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, et al. (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40: e49.
  38. 38. Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yi Chuan 29: 1023–1026.
  39. 39. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30: 2725–2729.
  40. 40. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420–3435.
  41. 41. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27: 297–300.
  42. 42. Yi F, Xie S, Liu Y, Qi X, Yu J (2013) Genome-wide characterization of microRNA in foxtail millet (Setaria italica). BMC Plant Biol 13: 212.
  43. 43. Khan Y, Yadav A, Suresh BV, Muthamilarasan M, Yadav CB, et al. (2014) Comprehensive genome-wide identification and expression profiling of foxtail millet [Setaria italica (L.)] miRNAs in response to abiotic stress and development of miRNA database. Plant Cell Tiss Organ Cult 118: 279–292.
  44. 44. Dai X, Zhao PX (2013) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39: W155–W159.
  45. 45. Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, et al. (2013) Facing growth in the European Nucleotide Archive. Nucleic Acids Res 41: D30–D35.
  46. 46. Patel RK, Jain M (2012) NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE 7: e30619.
  47. 47. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359.
  48. 48. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, et al. (2006) TM4 microarray software suite. Methods Enzymol 411: 134–193.
  49. 49. Saeed AI, Sharov V, White J, Li J, Liang W, et al. (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34: 374–378.
  50. 50. Suresh BV, Muthamilarasan M, Misra G, Prasad M (2013) FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research. PLoS ONE 8: e71418.
  51. 51. Gupta S, Kumari K, Sahu PP, Vidapu S, Prasad M (2013) Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv]. Plant Cell Rep 31: 323–337.
  52. 52. Pandey G, Misra G, Kumari K, Gupta S, Parida SK, et al. (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res 20: 197–207.
  53. 53. Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, et al. (2013) Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in millet and non-millet species. PLoS ONE 8: e67742.
  54. 54. Gupta S, Kumari K, Das J, Lata C, Puranik S, et al. (2011) Development and utilization of novel intron length polymorphic markers in foxtail millet (Setaria italica (L.) P. Beauv.) Genome. 54: 586–602.
  55. 55. Muthamilarasan M, Venkata Suresh B, Pandey G, Kumari K, Parida SK, et al. (2014b) Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet. DNA Res 21: 41–52.
  56. 56. Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34: W609–W612.
  57. 57. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151–1155.
  58. 58. Yang Z, Gu S, Wang X, Li W, Tang Z, et al. (2008) Molecular evolution of the cpp-like gene family in plants: insights from comparative genomics of Arabidopsis and rice. J Mol Evol 67: 266–277.
  59. 59. Muthamilarasan M, Bonthala VS, Mishra AK, Khandelwal R, Khan Y, et al. (2014) C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses. Funct Integr Genomics 14: 531–543.
  60. 60. Lata C, Sahu PP, Prasad M (2010) Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. Biochem Biophys Res Commun 393: 720–727.
  61. 61. Puranik S, Jha S, Srivastava PS, Sreenivasulu N, Prasad M (2011) Comparative transcriptome analysis of contrasting foxtail millet cultivars in response to short-term salinity stress. J Plant Physiol 168: 280–287.
  62. 62. Lata C, Bhutty S, Bahadur RP, Majee M, Prasad M (2011) Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet (Setaria italica (L.)). J Exp Bot 62: 3387–3401.
  63. 63. Le DT, Nishiyama R, Watanabe Y, Mochida K, Yamaguchi-Shinozaki K, et al. (2011) Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress. DNA Res 18: 263–276.
  64. 64. Longeman J, Schell J, Willmitzer L (1987) Improved method for the isolation of RNA from plant tissues. Anal Biochem 163: 16–20.
  65. 65. Kumar K, Muthamilarasan M, Prasad M (2013) Reference genes for quantitative Real-time PCR analysis in the model plant foxtail millet (Setaria italica L.) subjected to abiotic stress conditions. Plant Cell Tiss Organ Cult 115: 13–22.
  66. 66. Kelley LA, Sternberg MJE (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols 4: 363–371.
  67. 67. Katiyar A, Smita S, Lenka SK, Rajwanshi R, Chinnusamy V, et al. (2012) Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC Genomics 13: 544.
  68. 68. Matus JT, Aquea F, Arce–Johnson P (2008) Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes. BMC Plant Biol 8: 83.
  69. 69. Wilkins O, Nahal H, Foong J, Provart NJ, Campbell MM (2009) Expansion and diversification of the Populus R2R3–MYB family of transcription factors. Plant Physiol 149: 981–993.
  70. 70. Cao ZH, Zhang SZ, Wang RK, Zhang RF, Hao YJ (2013) Genome wide analysis of the apple MYB transcription factor family allows the identification of MdoMYB121 gene confering abiotic stress tolerance in plants. PLoS ONE 8: e69955.
  71. 71. Jiang C, Gu J, Chopra S, Gu X, Peterson T (2004) Ordered origin of the typical two– and three-repeat Myb genes. Gene 326: 13–22.
  72. 72. Rosinski JA, Atchley WR (1998) Molecular evolution of the Myb family of transcription factors: evidence for polyphyletic origin. J Mol Evol 46: 74–83.
  73. 73. Da G, Lenkart J, Zhao K, Shiekhattar R, Cairns BR, et al. (2006) Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc Natl Acad Sci U S A 103: 2057–2062.
  74. 74. Pao GM, Saier MH (1995) Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution. J Mol Evol 40: 136–154.
  75. 75. Chopra S, Athma P, Peterson T (1996) Alleles of the maize P gene with distinct tissue specificities encode Myb-homologous proteins with C-terminal replacements. Plant Cell 8: 1149–1158.
  76. 76. Grotewold E, Drummond BJ, Bowen B, Peterson T (1994) The myb-homologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset. Cell 76: 543–553.
  77. 77. Ponting CP, Blake DJ, Davies KE, Kendrick-Jones J, Winder SJ (1996) ZZ and TAZ: new putative zinc fingers in dystrophin and other proteins. Trends Biochem Sci 21: 11–13.
  78. 78. Roberts RG (2001) Dystrophins and dystrobrevins. Genome Biol 2: REVIEWS3006.
  79. 79. Dhalluin C, Carlson JE, Zeng L, He C, Aggarwal AK, et al. (1999) Structure and ligand of a histone acetyltransferase bromodomain. Nature 399: 491–496.
  80. 80. Ramakrishnan V, Finch JT, Graziano V, Lee PL, Sweet RM (1993) Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature 362: 219–223.
  81. 81. Sakai H, Aoyama T, Oka A (2000) Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators. Plant J 24: 703–711.
  82. 82. Wenkel S, Turck F, Singer K, Gissot L, Le Gourrierec J, et al. (2006) CONSTANS and the CCAAT box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis. Plant Cell 18: 2971–2984.
  83. 83. Gowik U, Burscheidt J, Akyildiz M, Schlue U, Koczor M, et al. (2004) cis-Regulatory elements for mesophyll-specific gene expression in the C4 plant Flaveria trinervia, the promoter of the C4 phosphoenolpyruvate carboxylase gene. Plant Cell 16: 1077–1090.
  84. 84. Yanagisawa S, Schmidt RJ (1999) Diversity and similarity among recognition sequences of Dof transcription factors. Plant J 17: 209–214.
  85. 85. Reyes JC, Muro–Pastor MI, Florencio FJ (2004) The GATA family of transcription factors in Arabidopsis and rice. Plant Physiol 134: 1718–1732.
  86. 86. Villain P, Mache R, Zhou DX (1996) The mechanism of GT element-mediated cell type-specific transcriptional control. J Biol Chem 271: 32593–32598.
  87. 87. Hobo T, Suwabe K, Aya K, Suzuki G, Yano K, et al. (2008) Various spatiotemporal expression profiles of anther-expressed genes in rice. Plant Cell Physiol 49: 1417–1428.
  88. 88. Chinnusamy V, Ohta M, Kanrar S, Lee BH, Hong X, et al. (2003) ICE1: a regulator of cold–induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev 17: 1043–1054.
  89. 89. Filichkin SA, Leonard JM, Monteros A, Liu PP, Nonogaki H (2004) A novel endo-beta-mannanase gene in tomato LeMAN5 is associated with anther and pollen development. Plant Physiol 134: 1080–1087.
  90. 90. Nishiuchi T, Shinshi H, Suzuki K (2004) Rapid and transient activation of transcription of the ERF3 gene by wounding in tobacco leaves: possible involvement of NtWRKYs and autorepression. J Biol Chem 279: 55355–55361.
  91. 91. Zhang ZL, Xie Z, Zou X, Casaretto J, Ho TH, et al. (2004) A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiol 134: 1500–1513.
  92. 92. Yadav CB, Muthamilarasan M, Pandey G, Prasad M (2014) Identification, characterization and expression profiling of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in foxtail millet. Plant Mol Biol Rep DOI:https://doi.org/ 10.1007/s11105-014-0736-y.