Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during seed development and in response to salt stress in peanut
- 350 Downloads
Plant basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses. However, systematic investigation and analyses of the bZIP gene family in peanut are lacking in spite of the availability of the peanut genome sequence.
In this study, we identified 50 and 45 bZIP genes from Arachis duranensis and A. ipaensis genomes, respectively. Phylogenetic analysis showed that Arachis bZIP genes were classified into nine groups, and these clusters were supported by several group-specific features, including exon/intron structure, intron phases, MEME motifs, and predicted binding site structure. We also identified possible variations in DNA-binding-site specificity and dimerization properties among different Arachis bZIPs by inspecting the amino acid residues at some key sites. Our analysis of the evolutionary history analysis indicated that segmental duplication, rather than tandem duplication, contributed greatly to the expansion of this gene family, and that most Arachis bZIPs underwent strong purifying selection. Through RNA-seq and quantitative real-time PCR (qRT-PCR) analyses, the co-expressed, differentially expressed and several well-studied homologous bZIPs were identified during seed development stages in peanut. We also used qRT-PCR to explore changes in bZIP gene expression in response to salt-treatment, and many candidate bZIPs in groups A, B, and S were proven to be associated with the salt-stress response.
This study have conducted a genome-wide identification, characterization and expression analysis of bZIP genes in Arachis genomes. Our results provide insights into the evolutionary history of the bZIP gene family in peanut and the funcntion of Arachis bZIP genes during seed development and in response to salt stress.
KeywordsbZIP gene family Peanut Evolution Expression analysis
ABRE binding factors
A insensitive 5
ABA-responsive element binding proteins
Basic leucine zipper
Days after flowering
Delay of germination
Hidden markov model
Multiple Em for Motif Elicitation
Open reading frames
Quantitative real-time PCR
Whole genome duplication
In plants, transcription factors (TFs) possess specific domains that bind upstream of target genes to regulate gene expression [1, 2]. Of these plant TFs, the basic leucine zipper (bZIP) transcription factor family is one of the largest, and was named and characterized based on the conserved bZIP domain [3, 4]. The domain is 60–80 amino acids in length and is composed of two parts: a basic region and a leucine zipper motif. The basic region is highly conserved and includes 16 amino acid residues with an invariant motif N-× 7-R/K-× 9, independently determining nuclear localization and DNA binding specificity [5, 6]. The leucine zipper motif is less conserved, and contains heptad repeats of leucine (Leu) or other bulky hydrophobic amino acids which is responsible for specific recognition and homo- and/or heterodimerization [4, 7]. The bZIP gene family has been systematically investigated and characterized based on the whole genome sequences of several plants, including Arabidopsis , rice , sorghum , maize , grapevine , Brachypodium distachyon , tomato , apple , cassava  and banana .
bZIP genes play important roles in many essential biological processes, including organ differentiation, flower and vascular development, embryogenesis, seed maturation and storage protein gene regulation [16, 17, 18, 19, 20]. Considerable evidence also indicates that bZIP genes are important regulators of signaling and the response to abiotic/biotic stress [4, 7]. The phytohormone abscisic acid (ABA) is associated with seed development as well as abiotic stress responses . The ABA-responsive element binding proteins (AREB) or ABRE binding factors (ABFs), which are group A bZIP proteins, have an important role in ABA and stress signaling [22, 23]. For instance, ABI5 is involved in ABA or stress signaling to regulate seed size and development, seed germination and early seedling growth as well as response to abiotic stress [24, 25, 26, 27]. Group B bZIP proteins, which have a transmembrane domain and a specific domain at the C-terminus, also are important to the salt stress response via endoplasmic reticulum stress signaling . For example, slbZIP38, a group G bZIP gene identified in tomato, have proven to be a negative regulator of salt stress tolerance . For Group S bZIP proteins, AtbZIP1, MtbZIP2, and MtbZIP26 from Arabidopsis thaliana and Medicago truncatula, were transcriptionally induced by salt treatment, leading to an increase in salt stress tolerance [30, 31, 32]. In addition, bZIPs from groups C and S could cooperate with several TFs to form heterodimers and be responsible for the salt stress and seed development crosstalk network . Together, these evidences indicate that bZIP genes have an essential role in both seed development and salt stress.
The peanut (Arachis hypogaea) is an important economical oilseed crop primarily grown in the tropics and semi-arid tropics and provide an important global source of vegetable oil and protein (http://faostat.fao.org/). Despite the economic and nutritional importance of peanuts, and the critical role of bZIP transcription factors in plant development and stress responses, only one AhbZIP gene has been reported that the over-expression of this gene (AREB1) is related to increase abiotic tolerance . In 2016, the genomes of the two diploid ancestors (A. duranensis and A. ipaensis) of cultivated peanut have become available , allowing the genome-wide identification and systematic analysis of the bZIP gene family in Arachis genomes. In this study, we identified bZIP genes and analyzed their bZIP domain sequences, gene structure and additional MEME motifs, the DNA-binding-site specificity and dimerization properties of the bZIP proteins. We also investigated the impact of segmental and tandem duplication on the expansion of Arachis bZIP gene family. Using the RNA-seq and quantitative real-time PCR (qRT-PCR) methods, we analyzed their expression profiles in seed developmental stages and salt stress, and identified several candidate Arachis bZIPs responsive to seed development and salt stress.
Identification of bZIP genes in A. duranensis and A. ipaensis genomes
The genomic sequences of A. duranensis and A. ipaensis and their annotated gene models were downloaded from peanutbase (http://www.peanutbase.org/). BLAST were firstly conducted to search homologous bZIP genes using known bZIP proteins from Arabidopsis , rice  and maize  as queries. The targeting genes with similarity of E-value less than 1e-5 were retained for the following analysis. Subsequently, Hidden Markov Model (HMM) search (http://hmmer.org/) of the bZIP domain profiles (PF00170, PF07716 and PF03131) were performed to identify bZIP domain in these candidate proteins. Finally, Interpro (http://prosite.expasy.org/) and ExPASy Proteomics Server (http://prosite.expasy.org/) were used to confirm the integrity of bZIP domain in candidate genes. Each bZIP gene was given a unique name based on the exact position on chromosome/scaffold (from top to bottom) (Additional file 1).
Sequence alignment and phylogenetic analysis
ClustalX 2.0  were used to align the bZIP sequences of coding DNA and proteins from A. thaliana, A. duranensis and A. ipaensis. The penalties for a gap open and gap extension were 10 and 0.1, respectively. PhyML 3.0 software  was used for the reconstruction of the maximum likelihood (ML) phylogenetic tree. The JTT + G model were determined to be the best model for phylogenetic tree construction according to the akaike information criterion implemented in ProtTest 3.0 . 100 replicates were used to produce bootstrap values. MEGA7  was used to edit and show the phylogenetic tree.
Gene structure of bZIP genes
The exon/intron structure of bZIP genes was analyzed and displayed using the GSDS platform (http://gsds.cbi.pku.edu.cn/) . Genewise  was used to determine the correspondence on coordinates between DNA (containing exon and intron together) and protein sequences. Then, the coordinates of bZIP domain in protein sequence were transformed to that in gene sequence using in-house perl scripts. The intron splicing phase within the basic and hinge regions of bZIP domains from all bZIP genes were characterized and divided into different types.
Detection of additional conserved motifs of bZIP genes
The MEME tool (http://meme.nbcr.net/meme/)  was employed to detect the additional motifs outside the bZIP domain of protein sequences. The motifs with 10–50 amino acids in length and E-value less than 1e - 40 were characterized. All the motifs were compared among bZIP genes to identify the group-conserved or group-specific signatures. These motifs were numbered according to their order in the protein sequences.
Detecting duplicated genes and estimation of nonsynonymous (Ka) and synonymous (Ks) substitutions per site and their ratios
MCScan (http://chibba.agtec.uga.edu/duplication/mcscan) was used to detect the duplicated genomic segments in two Arachis genomes. Tandem duplication cluster was defined to contain at least two consecutive genes with sequence similarity (threshold of e < 10− 20), and one unrelated gene among cluster members was tolerated. The amino acid sequences of duplicated gene pairs were firstly aligned and guide the alignment of cDNA sequences in-house perl-scripts. KaKs_Calculator was used to compute Ka and Ks values of each duplicated gene pair using the YN model .
Expression analysis of Arachis bZIP genes during seed development and under salt stress
For investigating the expression of bZIP genes during peanut seed development, we downloaded the previously reported RNA-seq data of peanut seeds at 20, 40 and 60 days after flowering (DAF) . Trimmomatic  was used to check, filter or trim RNA-seq reads with low-quality. RNA-seq reads were mapped to reference genome using Hisat2 , and the gene expression value were estimated using RSEM . DESeq2 package  was used for differential expression (DE) analysis.
For qRT-PCR experiment, the elite peanut cultivar ‘Zhonghua16’ was planted to collect seeds at DAF20, DAF40, and DAF60 according to the previous method . For preparing salt-stress plants, 2-week-old peanut seedlings (at the four-leaf stage) were removed from the soil and hydroponically grown in a 300 mM NaCl solution (Treatment) or deionized water (Control). The time points for salt treatment were setted to be 0, 1, 5, and 10 h, and the seedling roots were collected and frozen immediately in liquid nitrogen for RNA extraction.
Total RNA was extracted with RNAprep Pure Plant Kit (TIANGEN, China) and reverse transcribed into cDNA with cDNA Synthesis Kit (Thermo Fisher Scientific, USA) following the manufacturer’s instructions. qRT-PCR were performed in a 20 μL reaction volume using a CFX connect Real-Time System (Bio-Rad, Hercules, CA, USA) and Hieff qRCR SYBR Green Master Mix (YEASEN, Shanghai, China). The peanut Actin gene (Aradu.W2Y55) was used as the internal control, and the difference in relative target gene expression among the different experimental conditions was calculated using the 2-∆∆Ct method. Standard error was calculated among the three biological replicates of each experiment. Student’s t test was used to test the statistical significance of differences in relative target gene expression.
Results and discussion
Identification, phylogenetic analysis and group classification of bZIP genes in A. duranensis and A. ipaensis
Based on homology searches and domain verification, a total number of 50 and 45 unique bZIP genes were identified in A. duranensis and A. ipaensis genomes, respectively. The details for these genes, including gene ID, genomic position, domain composition, and group classification are given in Additional file 1. According to the existing nomenclature system, we assigned unique names to each of these novel bZIP genes: AdbZIP1–50 and AibZIP1–45. After checking bZIP domains, 93 genes had a typical bZIP domain, including an invariant N-× 7-R/K motif in the basic region and a heptad repeat of Leu positioned exactly nine amino acids upstream of R/K toward the C terminus (Additional file 2). The remaining two bZIP genes, AdbZIP28 and AibZIP22, had an unusual substitution in the basic region: a replacement of the conserved Arg/Lys (R/K) with IIe (I). This replacement has also been reported in other species [8, 49].
Gene structure of Arachis bZIP genes
As intron and exon organization might indicate the evolutionary trajectory of bZIP genes , we examined the structure of Arachis bZIP genes, including intron number, length, and splicing phase (Additional file 4). We found that overall gene structures were identical or similar for Arachis bZIPs within the same phylogenetic group. Considering the number of introns of peanut bZIPs, 24% of AdbZIPs and 22% of AibZIPs were intronless, occurring exclusively in groups S and B. Among the intron-containing genes, the number of introns varied from 1 to 13 in AdbZIP and AibZIP genes. bZIP genes in group G had the most introns, consistent with observations in other legume genomes .
The motif compositions for different groups of Arachis bZIPs
Arachis bZIP DNA-binding-site structure and dimerization properties
The core basic region and the hinge region of the bZIP domain independently determine DNA-binding specificity, as demonstrated by several experiments [5, 6]. The unusual replacement of the two invariant sites, asparagine (Asn/N; position: − 18) and arginine (Arg/R; position: − 10), altered DNA-binding specificities . We aligned the amino acids sequences of the basic and hinge regions of peanut bZIP proteins to identify conserved and polymorphic amino acid residues within each group (Additional file 6). No replacements of Asn/N at the − 18 position were observed in any peanut bZIPs. However, all members of group I had lysine (Lys/K) instead of arginine (R) at the − 10 position, consistent with the group I bZIPs from other legume species . In addition, AdbZIP28 and AibZIP22 (group U) had a hydrophobic isoleucine (Ile/I) residue instead of an arginine (Arg/R), and such a replacement was demonstrated to completely inhibit the affinity of bZIP for AP1 in yeast  and does not recognize G-boxes in rice .
At the a position, about 20% of the residues were asparagine (Asn/N), which can form a polar pocket in the hydrophobic interface, allowing for more stable N-N interactions at a↔a′ (the corresponding position in the opposite helix), as compared to other amino acids . Across the different heptads, the second and the fifth heptads had the highest frequency of Asn/N residues in the a position (61.46 and 60.22%, respectively; Fig. 4b). At the d position (Fig. 4a), the Leu was found in 45% of all peanut bZIPs and is one of the most dimer-stabilizing aliphatic amino acids . At the e position, 37% of all peanut bZIPs had acidic amino acids D or E, while at the g position, 44% of all peanut bZIPs had the basic amino acids R or K (Fig. 4a). These charged amino acids are thought to form salt bridges between helices in electrostatic interactions . The attractive or repulsive g↔e′ electrostatic interactions can also form interhelical salt bridges that affect dimerization specificity and stability . For investigating the contribution of charged residues at the e and g positions in governing dimerization properties of Arachis bZIP proteins, the frequencies of attractive and repulsive g↔e′ pairs in each heptad was calculated (Fig. 4c). Across all heptads, the attractive g↔e′ pairs were concentrated in the second (15.6%), fifth (35%) and sixth (30%) heptads, indicating they can form complete attractive g↔e′ interactions and contribute to stability through complementation in a heterodimer. Three groups comprising 28 subfamilies (BZ1–BZ28) were further divided based on homo- and heterodimerization properties, particularly dimerization specificity [60, 63] (Additional file 7).
The impact of whole genome duplication and tandem duplication on the expansion of Arachis bZIP gene family
We detected 35 AdbZIPs and 32 AibZIPs involved in duplicated genomic blocks, accounting for around 70% (35/50) and 71% (32/45) of the bZIP genes in each species (Fig. 5b and Additional file 8). Moreover, the duplicated bZIP gene pairs occurred either within a chromosome or between chromosomes, and some of these pairs were segmentally duplicated once, twice, or three times. This result indicated preferential gene retention and frequent chromosomal arrangements after WGD. Tandem duplications were detected for only two gene pairs (AdbZIP33/AdbZIP34 and AdbZIP41/AdbZIP42) in A. duranensis and only one gene pair (AibZIP28/AibZIP29) in A. ipaensis. This suggested that tandem duplication occurred rarely and was not more important than segmental duplication in the expansion of the bZIP gene family. We also used phylogenetic and syntenic analyses to identify 35 orthologous bZIP gene pairs between A. duranensis and A. ipaensis. These genes were also homeologs between the two subgenomes of the tetraploid peanut.
To understand the evolutionary constraints acting on the Arachis bZIP genes, we calculated Ka/Ks values for each duplicated bZIP gene pair in two Arachis species (Additional file 9). For most of these pairwise comparisons, the Ka/Ks values were less than 0.5 (only one pairwise comparison between duplicated AdbZIPs and only two between duplicated AibZIPs were larger than 0.5). This suggested that strong purifying selection acted on the Arachis duplicated bZIPs to remove deleterious mutations at the protein level.
Expression analysis of Arachis bZIP genes during peanut seed development
In group A, AdbZIP33 and AibZIP28 were orthologous to Arabidopsis ABA insensitive 5 (ABI5), which is associated with ABA-signaling as well as the regulation of seed development and longevity in Arabidopsis  and legumes . Our RNA-seq and qRT-PCR results showed that both orthologous ABI5 copies from the two subgenomes of the tetraploid peanut were highly expressed during development, suggesting the function of these genes may be similar in peanut and Arabidopsis. Our qRT-PCR results also indicated that the group A genes AdbZIP42, AdbZIP48 and AibZIP31 were stably expressed during development (Fig. 6b and Additional file 11). These genes are homologous to ABFs and AREB, which are involved in ABA-mediated seed development, germination, and embryo maturation . Three genes in group C (AdbZIP23, AdbZIP37, and AibZIP30) were also highly expressed, and are homologous to the maize bZIP factor Opaque2. Opaque2 regulates protein accumulation and amino acid and sugar metabolism in maize seeds [66, 67, 68, 69]. In addition, the group S genes AibZIP10, AdbZIP12, AdbZIP24, AdbZIP26, and AdbZIP36 were extremely highly expressed in peanut seeds (Fig. 6b and Additional file 11). Interestingly, the group S genes AdbZIP24 and AdbZIP36 had a similar expression pattern to the group C genes AdbZIP37 and AibZIP30: a decrease in expression level as seed development progressed.
We then further investigated the divergences in gene expression between homeologous genes from the AA and BB genomes of the tetraploid peanut. The heatmap analysis indicated that the overall expression patterns across seed development were similar for 31 pairs of homeologous/orthologous genes from the AA and BB genomes. We used the differential expression analysis method in combination with statistical methods to calculate differences in gene expression between these gene pairs for each sample. We found that 3 pairs of genes (AdbZIP5 and AibZIP5, AdbZIP17 and AibZIP15, AdbZIP46 and AibZIP41) were differentially expressed at 20 DAF, 3 pairs (AdbZIP3 and AibZIP1, AdbZIP4 and AibZIP4, AdbZIP49 and AibZIP45) at 40 DAF, and 5 pairs (AdbZIP3 and AibZIP1, AdbZIP33 and AibZIP28, AdbZIP37 and AibZIP30, AdbZIP10 and AibZIP10, AdbZIP1 and AibZIP3) at 60 DAF. These results indicated the overall expression conservation between two genomes, but suggested that 20% of the genes had diverged in expression during the parallel evolution and polyploidization of two genomes (Fig. 6c).
qRT-PCR expression profiles of Arachis bZIP genes under salt stress
Group A bZIPs possess the CKII and Ca2 + −dependent protein kinase phosphorylation site motifs involved in stress and/or ABA signaling, and these motifs are important for plant adaptation to various abiotic environmental stressors . Indeed, many group A genes are associated with the salt stress response. In Arabidopsis, ABI5 and ABFs/AREB are key ABA-dependent signal transduction factors involved in abiotic stress tolerance [22, 73]. The over-expression of GhABF2 significantly improved salt stress tolerance both in Arabidopsis and cotton . In tomato, slAREB1 and slbZIP1 knockout increased salt stress tolerance, while slAREB1 and slbZIP1 over-expression reduced salt stress tolerance [75, 76]. Here, genes AdbZIP42 and AibZIP35 were significantly up-regulated in response to salt stress, and these genes are homologous to ABFs, GhABF2, slAREB1, and slbZIP1. In addition, these genes have been reported to be phosphorylated by the ABA-activated SnRK2 protein kinases [77, 78, 79, 80], suggesting phosphorylating ABA response element-binding factors may be critical for the ABA-mediated salt stress response.
The group B genes AdbZIP45 and AibZIP40 were up-regulated after 10 h of salt stress, and these genes are homologous to AtbZIP17, which could improve the expression of several salt stress response genes in Arabidopsis . Seven group G bZIP genes (AdbZIP7, AdbZIP15, AdbZIP19, AdbZIP50, AibZIP17, AibZIP21, and AibZIP38) were homologous to Arabidopsis AtbZIP41 and tomato slbZIP38, and these genes have both been shown to negatively regulate salt stress . Of these seven genes, AdbZIP15 was significantly down-regulated after 1 h and 5 h of salt stress treatment, while AdbZIP19 and AibZIP17 were significantly up-regulated after 10 h of salt stress. Thus, AdbZIP15, AdbZIP19 and AibZIP17 might confer resistance to salt stress. AdbZIP15 might be a negative regulator of salt stress, as its expression pattern was similar to that of slbZIP38 in response to salt stress.
The group S genes AdbZIP24 and AdbZIP36 were homologous to AtbZIP1, AtbZIP53, MtbZIP2, and MtbZIP26, and the expression patterns of these genes in response to salt stress were similar (Fig. 7). In particular, AdbZIP36 was significantly up-regulated after 10 h of salt stress. Two homologous genes in Arabidopsis, AtbZIP1 and AtbZIP53, were shown to reprogram the primary carbohydrate and amino acid metabolism to help roots adapt to salt stress . The homologs MtbZIP2 and MtbZIP26 are also transcriptionally induced by salt treatment, and improve plant tolerance to salt stress . Notably, the expression pattern of AdbZIP36 was similar to those of AtbZIP1, MtbZIP2, and MtbZIP26 in Arabidopsis and M. truncatula [30, 32], suggesting that AdbZIP36 might be a positive regulator of tolerance to salt stress in the peanut. In summary, our study of expression analysis has identified several candidate peanut bZIPs, which may be associated with the salt-stress response, as targets for future research.
Despite the importance of bZIP transcription factors for plant growth, development, and abiotic stress responses, little is known about the bZIP gene family in peanut. Here, we used the previously published peanut reference genome to perform a comprehensive analysis of peanut bZIPs, including sequence identification, phylogenetic construction, motif composition characterization, gene structure analysis, and determination of DNA-binding-site specificity and dimerization properties. We also investigated evolutionary expansion of the bZIP gene family. bZIP genes were clearly divided into phylogenetic clades. These clades were supported by various group-specific sequence characteristics, including exon/intron structure, intron phases in domain, MEME motif composition, DNA-binding specificity, and dimerization properties. By analyzing changes in bZIP gene expression during seed development and in response to salt stress, we characterized the overall expression patterns for different groups of bZIPs. We also identified several candidate bZIP proteins that may be important for seed development and the salt stress response. The information generated in this study could facilitate further research on bZIP gene family and other gene families in peanut.
This research was supported by the National Key Research and Development Program of China (2018YFD1000900), the National Natural Science Foundation of China (nos. 31671734, 31461143022, 31770250 and 31371662), the Knowledge Innovation Program of Chinese Academy of Agricultural Sciences, Central Public-interest Scientific Institution Basal Research Fund, National High Technology Research and Development Program of China (863 Program, no. 2013AA102602), Agriculture Research System of China (CARS-14).
Availability of data and materials
All data generated or analyzed during this study are included in this published article and its supplementary information files.
ZW, YL and BL conceived the project and research plans, designed the experiments, and wrote the manuscript with contributions from all authors. LY, LW, DH, YK and LS performed the experiments. ZW analyzed the data and prepared figures, ZW, HJ, YL and BL revised the manuscript critically. All authors have read and approved the final version of the manuscript.
Ethics approval and consent to participate
Consent for publication
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
- 5.Suckow M, Schwamborn K, Kisters-Woike B, von Wilcken-Bergmann B, Muller-Hill B. Replacement of invariant bZip residues within the basic region of the yeast transcriptional activator GCN4 can change its DNA binding specificity. Nucleic Acids Res. 1994;22(21):4395–404.PubMedPubMedCentralGoogle Scholar
- 22.Kerr TCC, Abdel-Mageed H, Aleman L, Lee J, Payton P, Cryer D, Allen RD. Ectopic expression of two AREB/ABF orthologs increases drought tolerance in cotton (Gossypium hirsutum). Plant Cell Environ. 2018;41(5):898-07.Google Scholar
- 29.Pan Y, Hu X, Li C, Xu X, Su C, Li J, Song H, Zhang X, Pan Y. SlbZIP38, a Tomato bZIP Family Gene Downregulated by Abscisic Acid, Is a Negative Regulator of Drought and Salt Stress Tolerance. Genes. 2017;8(12):402.Google Scholar
- 30.Hartmann L, Pedrotti L, Weiste C, Fekete A, Schierstaedt J, Gottler J, Kempa S, Krischke M, Dietrich K, Mueller MJ, et al. Crosstalk between two bZIP signaling pathways orchestrates salt-induced metabolic reprogramming in Arabidopsis roots. Plant Cell. 2015;27(8):2244–60.PubMedPubMedCentralGoogle Scholar
- 33.Weltmeier F, Rahmani F, Ehlert A, Dietrich K, Schutze K, Wang X, Chaban C, Hanson J, Teige M, Harter K, et al. Expression patterns within the Arabidopsis C/S1 bZIP transcription factor network: availability of heterodimerization partners controls gene expression during stress response and development. Plant Mol Biol. 2009;69(1–2):107–19.PubMedGoogle Scholar
- 37.Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59(3):307–21.Google Scholar
- 39.Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–4.Google Scholar
- 53.Zhou Y, Xu D, Jia L, Huang X, Ma G, Wang S, Zhu M, Zhang A, Guan M, Lu K, et al. Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus. Genes. 2017;8(10):288.Google Scholar
- 64.Dekkers BJ, He H, Hanson J, Willems LA, Jamar DC, Cueff G, Rajjou L, Hilhorst HW, Bentsink L. The Arabidopsis DELAY OF GERMINATION 1 gene affects ABSCISIC ACID INSENSITIVE 5 (ABI5) expression and genetically interacts with ABI3 during Arabidopsis seed development. Plant J. 2016;85(4):451–65.PubMedGoogle Scholar
- 73.Uno Y, Furihata T, Abe H, Yoshida R, Shinozaki K, Yamaguchi-Shinozaki K. Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions. Proc Natl Acad Sci U S A. 2000;97(21):11632–7.PubMedPubMedCentralGoogle Scholar
- 74.Liang C, Meng Z, Meng Z, Malik W, Yan R, Lwin KM, Lin F, Wang Y, Sun G, Zhou T, et al. GhABF2, a bZIP transcription factor, confers drought and salinity tolerance in cotton (Gossypium hirsutum L.). Scientific Rep. 2016;6:35040.Google Scholar
- 77.Kobayashi Y, Murata M, Minami H, Yamamoto S, Kagaya Y, Hobo T, Yamamoto A, Hattori T. Abscisic acid-activated SNRK2 protein kinases function in the gene-regulation pathway of ABA signal transduction by phosphorylating ABA response element-binding factors. Plant J. 2005;44(6):939–49.PubMedGoogle Scholar
- 79.Yoshida T, Fujita Y, Maruyama K, Mogami J, Todaka D, Shinozaki K, Yamaguchi-Shinozaki K. Four Arabidopsis AREB/ABF transcription factors function predominantly in gene expression downstream of SnRK2 kinases in abscisic acid signalling in response to osmotic stress. Plant Cell Environ. 2015;38(1):35–49.PubMedGoogle Scholar
- 80.Yoshida T, Fujita Y, Sayama H, Kidokoro S, Maruyama K, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K. AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent ABA signaling involved in drought stress tolerance and require ABA for full activation. Plant J. 2010;61(4):672–85.PubMedGoogle Scholar
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.