http://orcid.org/0000-0001-5580-4127
Figures
Abstract
African oil palm (Elaeis guineensis) is an important oil crop grown in tropical region and sensitive to low temperature along with high tolerance to salt and drought stresses. Since the WRKY transcription factor family plays central roles in the regulation of plant stress tolerance, 95 genes belonging to the WRKY family were identified and characterized in oil palm genome. Gene structure analysis showed that EgWRKY genes have considerable variation in intron number (0 to 12) and gene length (477bp to 89,167 bp). Duplicated genes identification indicated 32 EgWRKY genes originated from segmental duplication and two from tandem duplication. Based on transcriptome data, most EgWRKY genes showed tissue-specific expression patterns and their expression could be induced under cold stress. Furthermore, six EgWRKY genes with more than two-folded increased expression level under cold stress were validated by RT-qPCR, which has higher expression level in cold, drought and high salinity treatment. The identification and characterization of WRKY gene family showed that EgWRKY were associated with a wide range of abiotic stress responses in Elaeis guineensis and some EgWRKY members with high expression levels could be selected for further research in analyzing their functions in the stress response in African oil palm.
Citation: Xiao Y, Zhou L, Lei X, Cao H, Wang Y, Dou Y, et al. (2017) Genome-wide identification of WRKY genes and their expression profiles under different abiotic stresses in Elaeis guineensis. PLoS ONE 12(12): e0189224. https://doi.org/10.1371/journal.pone.0189224
Editor: Maoteng Li, Huazhong University of Science and Technology, CHINA
Received: June 8, 2017; Accepted: November 21, 2017; Published: December 11, 2017
Copyright: © 2017 Xiao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the paper and its Supporting Information files.
Funding: This work was supported by the Scientific and Technological Cooperation Projects of Hainan province (No. SQ2015GJXM0076) and the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences (1630152016006).
Competing interests: The authors have declared that no competing interests exist.
Introduction
African oil palm (2n = 32, Elaeis guineensis), belonging to the family Arecaceae, is a major tropical oil crop worldwide, which has the highest oil production per unit area. Presently, this tropical crop is cultivated in Southeast Asia, Africa, Central America and Brazil. In 2012, the total yield of African oil palm was approximately 50 million tons of palm oil from 17 million hectares of plantation (http://faostat3.fao.org/home/E). The whole-genome sequence of Elaeis guineensis was completed and released in2013 and a total of 1.53 Gb of sequence data was assembled with 34,802 genes annotated [1]. As a tropical oil crop, Elaeis guineensis is particularly sensitive to low temperature but has high tolerance to salt and drought stresses. Identifying and validating genes related with stress response processes in African oil palm especially for cold responsive process will assist the further molecular breeding of stress tolerance cultivars.
WRKY genes have been identified and functionally analysed in various species. A large proportion of WRKY genes were found to be involved in various biotic [2–7] and abiotic stresses [8–14]. The expression of WRKY gene can also be induced by abscisic acid [15], gibberellins (GA) [16], salicylic acid [17], jasmonic acid [18], and ethylene treatment [19]. In Arabidopsis, the expression of AtWRKY30can be induced by abiotic stress and methyl viologen (MV), H2O2, arsenic, drought, NaCl, and mannitol treatment. Over-expression ofAtWRKY30can significantly increase the tolerance of Arabidopsis to MV and salinity stress [20]. Meanwhile, some WRKYs in rice were also found to be associated with abiotic stress, including OsWRKY11 [11], OsWRKY30[14], OsWRKY45[21], and OsWRKY47 [22]. Mutation of WRKY46 can decrease the tolerance to osmotic and salt stress in Arabidopsis [23]. The expression levels of WRKY25 and WRKY26 can be up-regulated by heat stress [24]. Moreover, in Arabidopsis, WRKY53 was validated in negative regulation of leaf senescence [25]. Some WRKY proteins were also shown to be phosphorylated by MAPKs and to contain a conserved motif for this phosphorylation [14]. Identification and characterization of WRKY genes in African oil palm could show a clue for genes involved in its stress responsive processes.
The WRKY transcription factors generally contain one or two conserved WRKY domains and a zinc finger motif and could be divided into three large clusters based on the variations in WRKY and zinc finger motifs [26]. Members of cluster I contain two conserved WRKY motifs with a C2H2 motif. ClustersII and III are characterized by a single conserved WRKY motif. The functional amino acid sequence of a WRKY motif is WRKYGQK and existed different variations, including WRKYGKK, WRKYGEK, WRKYGRK, WKKYGQK, WKRYGQK, and WSKYEQK. Meanwhile, there are two types of zinc finger motifs in WRKY transcription factors: the C2H2 motif (C-X4-5-C-X22-23-H-X1-H) and the C2HC motif (C-X5-7-C-X2-3-H-X1-C) [26].
To date, many WRKY genes in different species have been identified, including 74 WRKY genes in Arabidopsis [27], 103 in rice [28], 45 in barley [29], 55 in cucumber [30], 119 in maize [31], 182 in soybean [32], 109 in cotton [33], and 85 in cassava [34]. However, there is still no systematic identification and characterization of WRKYs conducted in African oil palm to find a clue for candidate WRKY genes involved in the stress responsive processes. In this study, genome-wide scanning for WRKY genes in African oil palm were conducted based on its genome sequence and the gene structures, phylogenetic relationships, expression profiles for all WRKY genes were also been performed. This research will provide insight into the functionality of EgWRKYs in this tropical oil crop.
Plant materials and methods
Plant materials and stress treatments
The seedlings of African oil palm (pisifera, thin-shelled) were grown in nurseries before stress treatments. Thirty-six oil palm plants germinated in the same week and grown in the same nursery were selected for subsequent cold, drought and salt treatment. The control seedlings for the three kinds of treatment were grown under 16 hours light/8 hours dark photoperiod at 26°C and three biological replicates were set in each stress treatment. For the cold treatment, a set of 12 seedling was placed in a growth chamber at 26°C for one day. Three oil palm plants were used as controls and the rest nine oil palm plants were kept at 8°C for 4, 24, and 48 hours under 16 hours light/8 hours dark photoperiod. Spear leaves were sampled from control and cold-treated seedlings and immediately frozen in liquid nitrogen. For the drought treatment, when soil water content reached 23% (2.3 g water per 10 g soil), spear leaves were sampled after 0, 4, 24 and 48 hours and immediately frozen in liquid nitrogen. For the salt treatment, the roots of oil palm seedlings were soaked in a NaCl solution (400 mmol/L)under 16 hours light/8 hours dark photoperiod at 26°C, and spear leaves were sampled 0, 4, 24, and 48 hours after salt treatment and immediately frozen in liquid nitrogen for RNA isolation. The MRIP method was used to extract RNA from these leaves [35].
Identification and phylogenetic analysis of EgWRKYs
The whole-genome sequence of Elaeis guineensis was downloaded from the National Center for Biotechnology Information (NCBI). Sequences of AtWRKY genes were downloaded from the Arabidopsis Information Resource (TAIR), available at http://www.arabidopsis.org. To identify EgWRKYs in Elaeis guineensis, AtWRKY sequences were used as queries to blast against all gene models in African oil palm, using a cutoff E-value of 1e-10. Multiple protein sequences alignment was used to confirm the conserved domains of EgWRKY sequences. Meanwhile, the conserved motifs were also predicted by alignment with CDD (http://www.ncbi.nlm.nih.gov/cdd) and PFAM databases (http://pfam.sanger.ac.uk). The MEME program (http://meme-suite.org) was used to identify the conserved motifs of EgWRKYs. MEGA 5.0 software was used to construct a neighbour-joining phylogenetic tree based on amino acid sequences of conserved WRKY domain with 1000 bootstrap replicates [36, 37].
Characterization of gene structures and gene duplication events of EgWRKY
The gene annotation summaries, CDSs, and mRNA sequences of Elaeis guineensis was downloaded from NCBI. Gene structures of EgWRKYs in Elaeis guineensis were confirmed by aligning mRNA sequences with the whole-genome sequence of Elaeis guineensis. The gene structures were identified by the Gene Structure Display Server programme. The duplication events of all EgWRKY identified in this study were analysed using an algorithm that can scan multiple genomes or subgenomes to identify putative homologous chromosomal regions and align these regions using genes as anchors [38].
The expression profiles analysis of EgWRKYs based on transcriptome datasets
The raw data of nine transcriptomes from different tissues, including mesocarp (five different developmental stages), leaf, fruit, flower, root, and shoot, were downloaded from the SRA (Sequence Read Archive) database of the NCBI website. RPKM (reads per kb per million reads)values were used to calculate gene expression levels using the following formula[39]:
where C is the number of reads that aligned exclusively with one expressed sequence; N is the total number of reads that aligned with all expressed sequences; and L is the number of bases in the CDS of the corresponding sequence.
Real-time qPCR assays
Quantitative real-time PCR was carried out using a standard SYBR Premix Ex Taq™ kit (TaKaRa) protocol in 96-well optical plates (Axygen) with a final reaction volume of 10 μl. The real-time qPCRs were incubated in 0.2-ml tubes in a Mastercycler ep realplex4 (Eppendorf) machine as follows: 95°C for 5 seconds, 55°C for 15 seconds and 68°C for 20 seconds. The procedure ended with a melt curve ramping from 60 to 95°C for 20 minutes to verify the PCR specificity. All qPCRs were carried out in biological and technical triplicate. The final Ct values were the means of nine measurements. The expression levels of the selected EgWRKYs were normalized to those of ELF, which was previously found to be a stable reference gene under abiotic stress [40]. One-way ANOVA was used to test significant difference (LSD, p< 0.05) of expression level between different time periods after cold, drought and salt treatment. All expression data was analyzed using SPSS software.
Results
Identification of EgWRKY transcription factors in the genome of Elaeis guineensis
The identification of EgWRKY genes in African oil palm were using the amino acid sequences of 72 AtWRKY genes were used as query sequences with a cutoff E-value < 10-5via BLAST analysis. The blast results showed that 97orthologous genes of AtWRKY were found in home-made database containing all protein coding genes from African oil palm and these genes could be classified into the EgWRKY gene family. The conserved WRKY domain sequences analysis in these EgWRKY genes excluded two genes from further analysis due to a lack of the conserved WRKY domain. These remaining EgWRKYs were designated from EgWRKY01 to EgWRKY95 according to their genomic location in African oil palm. Detailed information about the 95 EgWRKY genes was listed in Table 1 (S1 and S2 Text).
Chromosomal locations, gene structures, and gene duplication of EgWRKY
The distribution of EgWRKY in African oil palm was uneven: 83EgWRKY genes were unevenly distributed among13 chromosomes; while no EgWRKY genes were detected in chromosomes12, 13 and 16 (Fig 1). Chromosome 1 harboured 14EgWRKY genes, the largest number of any chromosome. Moreover, 12EgWRKYgenes were located on undetermined chromosomes.
Vertical bars represent chromosomes of Elaeis guineensis. The chromosome number is indicated at the top of each chromosome. The coloured lines indicate different clusters based on multiple alignments between conserved WRKY domains from the 95 EgWRKY genes identified in this study. Dark red: cluster I; Green: cluster II; Blue: cluster III; Yellow: cluster IV; Red: cluster V; Black: cluster VI; Purple: cluster VII; Brown: cluster VIII; Bright green: cluster IX.
Analysis of EgWRKY gene structures indicated a notably variation exist in these genes (Fig 2). The intron numbers of EgWRKY genes identified in this study varied from 0 to 12, with an average of 2.99 introns per EgWRKY (S1 Table). The largest fraction of EgWRKYs (42, 44.21%) contained two introns, followed by EgWRKYs containing three introns (20, 21.05%). Large gene size variation were detected in EgWRKY which varied from 477 bp (EgWRKY08) to 89,167 bp (EgWRKY71), with an average size of 5992 bp. The large variations in structure in the members of the EgWRKY gene family suggest that the genome of Elaeis guineensis has undergone significant divergence during a long evolutionary history.
Exons are represented by coloured boxes and introns are represented by black lines.
The segmental duplication in Elaeis guineensis defined this species may have originated from a palaeotetrapolyploid. In this study, we investigated the segmental duplication event shappened in blocks containing EgWRKYs genes. The gene distribution in oil palm homologous blocks showed that 32 EgWRKYs were produced by segmental duplication, and two EgWRKYs were produced by tandem duplication. According to whole-genome duplication analysis of Elaeis guineensis, four large synteny blocks were detected in chromosomes 1, 3, 6, and 7. The 32 EgWRKYs produced by segmental duplication were also found to be located in the four large synteny blocks indicated by Singh et al [1] (Fig 3). Nine pairs of EgWRKYs in chromosomes 1 and 6 showed good collinear relationships. Seven other pairs of EgWRKYs produced by segmental duplication were detected in chromosomes 3 and 7.
The coloured bars represent chromosomes of Elaeis guineensis.
Classification of EgWRKYs according to conserved WRKY domains
Of the 95 EgWRKYs identified, the majority(67, 70.52%)contained only one conserved WRKY domain, 19 (20%) contained two conserved WRKY domains, and the remaining 9 (9.48%)contained one conserved C2H2-type zinc finger domain and one conserved WRKY domain (Fig 4). Phylogenetic analyses were performed to evaluate the relationship between the identified EgWRKYs by the neighbour-joining analysis. The phylogenetic tree was constructed based on the WRKY motif, and 95 EgWRKY genes were classified into eight groups (Fig 5). The 67 EgWRKYs that contained only one WRKY domain clustered into all groups except V and VI. The N-terminal WRKY domains in the19 EgWRKYs containing two conserved WRKY domains clustered into group I, except for EgWRKY92, EgWRKY93, EgWRKY67, and EgWRKY70, while the other C-terminal WRKY domains were clustered exclusively into groups V and VI. Meanwhile, the EgWRKYs containing one conserved C2H2-type zinc finger domain and one conserved WRKY domain were clustered into groupVII, except for EgWRKY09, EgWRKY37, EgWRKY38, and EgWRKY85.
All motifs were identified by MEME with the full-length amino acid sequence of 95 EgWRKY in Elaeis guineensis. The size of each EgWRKY were displayed proportionally. WRKY and bZIP motif were indicated using different colour box.
EgWRKYs that contain only one WRKY domain are marked with brown circles; EgWRKYs that contain conserved WRKY and bZIP domains are marked with red circles; EgWRKYs that contain two conserved WRKY domains are marked with blue circles.
Expression levels of EgWRKYs in different tissues based on transcriptome data
To assess EgWRKY expression levels in different tissues of Elaeis guineensis, nine transcriptomes were downloaded from the SRA database of NCBI. These transcriptomes covered six oil palm tissues, including mesocarp (five different developmental stages), leaf, fruit, flower, root and shoot tissue. Almost every EgWRKY gene expressed (RPKM value > 0) in at least one transcriptome data set, except for EgWRKY08, EgWRKY09, EgWRKY37, EgWRKY38, EgWRKY40, EgWRKY46and EgWRKY85 (Fig 6). However, a large proportion of EgWRKYs showed low expression levels in the nine transcriptome data sets (RPKM values< 15). EgWRKY19had high expression levels (RPKM value > 15) in all five tissues of Elaeis guineensis. Three EgWRKYs had high expression levels (RPKM value >15) in four tissues (including EgWRKY69, EgWRKY07 and EgWRKY19). Thirty EgWRKYs showed high expression levels (RPKM value >15) in only one tissue (including EgWRKY01, 02, 05, 06, 11, 20, 21, 24, 25, 30, 31, 33, 35, 36, 41, 44, 48, 49, 51, 53, 58, 60, 64, 66, 67, 74, 80, 81, 93 and94), which indicated that a large proportion of EgWRKYs showed a tissue-specific expression pattern. Twenty-nine EgWRKYs had low (RPKM value < 15)or no expression in the five tissues of Elaeis guineensis (including EgWRKY08, 09, 10, 12, 13, 15, 17, 23, 32, 37, 38, 39, 40, 42, 46, 47, 50, 52, 63, 65, 68, 75, 78, 79, 82, 90, 92 and95).
Log 2RPKM values were used to construct the heat map with clustering.
Meanwhile, we also investigated the expression patterns of the duplicated gene pairs in different tissues. As shown in Fig 7, the expression levels of most duplicated gene pairs showed different patterns across different tissues, except for WRKY24_Chr3/WRKY56_Chr7 in flower tissue andWRKY26_Chr3/WRKY59_Chr7 in flower and root tissue. These two duplicated gene pairs both showed high expression levels in flower and root tissue. These results suggested that subfunctional processes have conducted in these duplicate gene pairs of EgWRKY during a long evolutionary history.
Expression changes of EgWRKYs under cold stress
Analysis of the expression level change of EgWRKYs under cold stress were conducted based on two transcriptomes: one from a control sample and one from a mixture of samples collected at different times after cold treatment. The RPKM values of all 95 EgWRKYs were increased in the trascriptome under cold stress. Additionally, the expression changes of 17 EgWRKYs were greater than two-fold under cold stress; these included EgWRKY03, 06, 07, 11, 16, 25, 26, 28, 29, 35, 52, 59, 61, 72, 76, 80 and 88.
Validation of expression of some EgWRKYs under cold, drought and salt stress
Based on trasncriptome data under cold treatment, 17 EgWRKY genes had increased expression levels at least two fold, six (EgWRKY06, 11, 25, 61, 72, and 88) of which were validated using real-time qRT-PCR. As was observed in the transcriptome data under cold stress, the expression of the six EgWRKYs could be induced under cold stress (Fig 8) which in accordance with the result from transcriptome data. Meanwhile, these six EgWRKYs could also be induced under drought and salt treatment. These data seem to indicate that these six EgWRKYs were associated with a wide range of abiotic stress responses in Elaeis guineensis.
One-way ANOVA was used to test significant difference of expression level between adjacent time periods. * indicated “p< 0.05” and ** indicated “p< 0.01”.
Discussion
African oil palm (Elaeis guineensis, 2n = 32) is an important tropical oil crop and has high tolerance to drought and salt stress. Currently, African oil palm is mainly cultivated in the tropics with a minimal growth temperature of 15°C and the cultivation area is limited. Low temperature causes cold damage such as yellowing and withering of young leaves and flowers in oil palm. To provide clues for molecular basis of oil palm stress response, the WRKY transcript factor family, which plays a critical role in the regulation of plant stress tolerance, was systematically analyzed in this study. A total of 95 EgWRKY genes were identified in African oil palm genome and characterized in four aspects—gene structure variation (477 bp in EgWRKY08 to 89,167 bp in EgWRKY71), phylogenetic relationship, gene expansion and expression profiles.
According to the amino acid sequences of the conserved domains, phylogenetic and evolutionary relationships among the 95 EgWRKYs were established. Previous studies had shown that WRKY transcription factors can be grouped into three clusters. Cluster I proteins contain two conserved WRKY motifs with a C2H2 motif. Clusters 2 and 3 are characterized by a single conserved WRKY motif[26]. A few studies also showed that in some species, the WRKY family may include cluster IV, which contains an incomplete WRKY domain [41]. In this study, 95 EgWRKYs were classified into nine clusters. For the N- and C-terminal WRKY conserved domains, the phylogenetic analysis showed that they were classified into different classes: N-terminal conserved domains were grouped into cluster I, and C-terminal domains were grouped into clusters V and VI. WRKY genes with conserved WRKY and bZIP motifs were grouped into cluster VII. WRKYs with single conserved motif were mainly grouped into clusters II, III, IV, VIII, and IX. EgWRKY13, EgWRKY40, and EgWRKY74, which were found to contain incomplete conserved motifs, were grouped into clusters II, VIII, and IX, respectively.
Gene structure diversity was thought to be able to reflect the evolutionary relationships of gene families, providing additional information for phylogenetic classification [42]. In this study, the numbers of introns found in the identified EgWRKY genes varied from 0 to 12, with an average of 2.99 introns per EgWRKY. Some previous studies have shown the diversity of gene structure in various species. The number of introns of cassava varied from 1 to 5[34]. In rice and rubber tree, the number of introns varied from 0 to 8 and 1 to 7, respectively[43, 44]. These results indicated that oil palm had more gene structure diversity than did cassava, rice and rubber tree. Meanwhile, the largest fraction of EgWRKYs (42, 44.21%) contained two introns. A similar phenomenon was also detected in cassava (42 of 85 MeWRKY genes contained two introns), rice (42 of 92) and rubber tree (40 of 81). Cluster I members contained 1 to 12 introns; cluster II, 3 to 6; cluster III, 2 to 4; cluster IV, 0 to 3; cluster V, 1 to 12; cluster VI, 0 to 6; cluster VII, 2 to 3 with the exception ofEgWRKY71; and clustersVIIIandIX, 2 to 3. Previous research showed that intron loss occurs more rapidly than intron gain after segmental duplication in rice. Consequently, some EgWRKYs from clusters I and V may be original genes compared to other EgWRKYs in Elaeis guineensis.
Some previous studies showed that the expression of WRKY transcription factors can be induced by abiotic stress and play crucial roles in regulating plant responses to abiotic stress [8–14]. In Arabidopsis, WRKY34 was found to be involved in cold stress and is a negative regulator of cold response[45]. AtWRKY34 showed high similarity toEgWRKY18 andEgWRKY64. Based on transcriptomic data, expression of EgWRKY18 andEgWRKY64 can be induced under cold stress. In Arabidopsis, AtWRKY30expression can be induced by abiotic stress and MV, H2O2, arsenic, drought, NaCl, and mannitol treatment. Overexpressing AtWRKY30can significantly increase the tolerance of Arabidopsis to MV and salinity stress[14]. AtWRKY30 showed high similarity to EgWRKY07 and EgWRKY52. According to transcriptome data, expression of these two EgWRKYs was strongly induced, up-regulated 3.367- and 11.883-fold, respectively. The C-terminal domain of AtWRKY33 can interact with multiple VQ proteins to regulate multiple abiotic stresses [10]. AtWRKY33has high similaritytoEgWRKY34and EgWRKY42, and these two EgWRKYs were up-regulated 2.72- and 1.15-fold under cold treatment, respectively. Based on transcriptome data and qPCR results, the expression of almost all the EgWRKYs was induced under abiotic stresses. This indicated that EgWRKYs may play important roles in oil palm responses to abiotic stresses.
Supporting information
S1 Text. Gene sequences of 95 EgWRKYs identified in the study.
https://doi.org/10.1371/journal.pone.0189224.s001
(TXT)
S2 Text. Amino acid sequence of 95 EgWRKYs identified in the study.
https://doi.org/10.1371/journal.pone.0189224.s002
(TXT)
S1 Table. Exon position of every EgWRKY gene in the chromosome of Elaeis guineensis.
https://doi.org/10.1371/journal.pone.0189224.s003
(XLSX)
References
- 1. Singh R, Ong-Abdullah M, Low E-TL, Manaf MAA, Rosli R, Nookiah R, et al. Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature. 2013;500:335–339. pmid:23883927
- 2. Mukhtar MS, Deslandes L, Auriac MC, Marco Y, Somssich IE. The Arabidopsis transcription factor WRKY27 influences wilt disease symptom development caused by Ralstonia solanacearum. Plant Journal. 2008;56:935–947. pmid:18702671
- 3. Tao Z, Liu HB, Qiu DY, Zhou Y, Li XH, Xu CG, et al. A pairs of allelic WRKY genes play opposite roles in rice bacteria interactions. Plant Physiol. 2009; 151:936–948. pmid:19700558
- 4. Marchive C, Mzid R, Deluc L, Barrieu F, Pirrello J, Gauthier A, et al. Isolation and characterization of a Vitis vinifera transcription factor, VvWRKY1, and its effect on responses to fungal pathogens in transgenic tobacco plants. J Exp Bot. 2007;58:1999–2010. pmid:17456504
- 5. Gallou A, Declerck S, Cranenbrouck S. Transcriptional regulation of defence geness and ivolvement of the WRKY transcription factor in arbuscular mycorrhizal potato root colonization. Funct Integr Genomics. 2012;12:183–198. pmid:21811781
- 6. Yang PZ, Chen CH, Wang ZP, Fan BF, Chen ZX. A pathogen- and salicylic acid-induced WRKY DNA-binding activity recognizes the elicitor response element of the tobacco class I chitinase gene promoter. Plant J. 1999;18: 141–149.
- 7. Wang YN, Dang FF, Liu Q, Wang X, Eulgem T, Lai Y. CaWRKY58, encoding a group I WRKY transcription factor of Capsicum annuum, negatively regulates resistance to Ralstonia solanacearum infection. Mol Plant Pathol. 2013; 14:131–144. pmid:23057972
- 8. Zhou XF, Wang GD, Sutoh K, Zhu JK, Zhang WX. Identification of cold-inducible microRNAs in Plants by transcriptome analysis. Bba-gene Regul Mech. 2008; 1779:780–788.
- 9. Zou C, Jiang W, Yu D. Male gametophyte-specific WRKY34 transcription factor mediates cold sensitivity of mature pollen in Arabidopsis. Journal of Experimental Botany. 2010; 61:3901–3914. pmid:20643804
- 10. Jiang YQ, Deyholos MK. Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses. Plant Mol Biol. 2009; 69:91–105. pmid:18839316
- 11. Wu X, Shiroto Y, Kishitani S, Ito Y, Toriyama K. Enhanced heat and drought tolerance in transgenic rice seedling overexpressing OsWRKY11 under the control of HSP101 promoter. Plant Cell Rep. 2009; 28:21–30. pmid:18818929
- 12. Ren XZ, Chen ZZ, Li Y, Zhang HR, Zhang M, Liu QA, et al. ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis. Plant J. 2010; 63:417–429. pmid:20487379
- 13. Jiang YJ, Liang G, Yu DQ. Activated expression of WRKY57 confers drought tolerance in Arabidopsis. Mol Plant. 2012; 5:1375–1388. pmid:22930734
- 14. Shen HS, Liu CT, Zhang Y, Meng XP, Zhou X, Chu CC, et al. OsWRKY30 is activated by MAP kinases to confer drought tolerance in rice.Plant Mol Biol. 2012; 80:241–253. pmid:22875749
- 15. Yu S, Ligang C, Liping Z, Diqiu Y. Overexpression of OsWRKY72 gene interferes in the abscisic aci signal and auxin transport pathway of Arabidopsis. J Biosci. 2010; 35: 459–471. pmid:20826955
- 16. Xie Z, Zhang Z, Zou X, Yang G, Komatsu S, Shen Q. Interactions of two abscisic-acid induced WRKY genes in repressing gibberellins signaling in aleurone cells. Plant J.2006; 46:231–242. pmid:16623886
- 17. Chen C, Chen Z. Isolation and characterization of two pathogen- and salicylic acid-induced genes encoding WRKY DNA-binding proteins from tobacco. Plant Mol Biol. 2000; 42:387–396. pmid:10794538
- 18. Rabara RC, Tripathi P, Lin J, Rushton PJ. Dehydration-induced WRKY genes from tobacco and soybean respond to jasmonic acid treatments in BY-2 cell culture. Biochemical and Biophysical Research Communications. 2012; 431:409–414.
- 19. Yang B, Jiang Y, Rahman MH, Dcyholos MK, Kav NN. Identification and expression analysis of WRKY transcription factor genes in canola (Brassica napus L.) in response to fungal pathogens and hormone treatments. BMC Plant Biol. 2009; 9:68. pmid:19493335
- 20. Scarpeci T, Zanor MI, Mueller-Roeber B, Valle EM. Overexpression of AtWRKY30 enhences abiotic stress tolerance during early growth stages in Arabidopsis thaliana. Plant Mol BIol. 2013; 83:265–277. pmid:23794142
- 21. Qiu Y, Yu D. Over-expression of the stress-induced OsWRKY45 enhances disease resistance and drought tolerance in Arabidopsis. Environmental & Experimental Botany. 2009; 65:35–47.
- 22. Raineri J, Wang S, Peleg Z, Blumwald E, Chan RL. The rice transcription factor OsWRKY47 is a positive regulator of the response to water deficit stress. Plant Molecular Biology. 2015; 88:401–413. pmid:25957211
- 23. Hu Y, Dong Q, Yu D. Arabidopsis WRKY46 coordinates with WRKY70 and WRKY53 in basal resistance against pathogen Pseudomonas syringae. Plant Sci. 2012; 185:288–297. pmid:22325892
- 24. Li S, Fu Q, Huang W, Yu D. Functional analysis of an Arabidopsis transcription factor WRKY25 in heat stress. Plant Cell Rep. 2009; 28:683. pmid:19125253
- 25. Xie Y, Huhn K, Brandt R, Potschin M, Bieker S, Straub D. REVOLUTA and WRKY53 connect early and late leaf development in Arabidopsis. Development. 2014;141: 4772–4783. pmid:25395454
- 26. Eulgem T, Rushton PJ, Robatzek S, Somssich IE. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 2000; 5:199–206. pmid:10785665
- 27. Ulker B, Somssich IE. WRKY transcription factors: from DNA binding towards biological function. Curr Opin Plant Biol. 2004; 7:491–498. pmid:15337090
- 28. Ramamoorthy R, Jiang SY, Kumar N, Venkatesh PN, Ramachandran S. A comprehensive transcriptional profiling of the WRKY gene family in rice under various abiotic and phytohormone treatments. Plant Cell Physiol. 2008; 49:865–879. pmid:18413358
- 29. Mangelsen E, Kilian J, Berendzen KW, Kolukisaoglu UH, Harter K, Jannsson C. Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained function between monocots and dicots. BMC Genomics. 2008; 9:194. pmid:18442363
- 30. Ling J, Jiang W, Zhang Y, Yu H, Mao Z, Gu X. Genome-wide analysis of WRKY gene family in Cucunis sativus. BMC Genomics. 2011; 12:471. pmid:21955985
- 31. Wei KF, Chen J, Chen YF, Wu LJ, Xie DX. Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize. DNA Res. 2012; 19:153–164. pmid:22279089
- 32. Bencke-Malato M, Cabreira C, Wiebke-Strohm B, Bucker-Neto L, Mancini E, Osorio MB. Genome-wide annotation of the soybean WRKY family and functional characterization of gene involved in response to Phakopsora pachyrhizi infection. BMC Plant Biol. 2014; 14:236. pmid:25201117
- 33. Fan X, Guo Q, Xu P, Gong Y, Shu H, Yang Y. Transcriptome-wide identification of salt-responsive members of WRKY gene family in Gossypium aridum. PLOS ONE. 2015; 10:e0126148. pmid:25951083
- 34. Wei Y, Shi H, Xia Z, Tie W, Ding Z, Yan Y. Genome-wide identification and expression analysis of the WRKY gene family in Cassava. Front Plant Sci. 2016; 7:25. pmid:26904033
- 35. Xiao Y, Yang Y, Cao H, Fan H, Ma Z, Lei X. Efficient isolation of quality RNA from tropical palms for RNA-seq analysis. Plant Omics. 2012; 5:584–589.
- 36. Larkin MA, Blackshield G, Brown NP, Chenna R, McGettigan PA, McWillian H. Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23:2947–2948. pmid:17846036
- 37. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011; 28:2731–2739. pmid:21546353
- 38. Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X. MCScan X: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40:e49. pmid:22217600
- 39. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods.2008; 5:621–628. pmid:18516045
- 40. Xia W, Mason AS, Xiao Y, Liu Z, Yang Y. Analysis of multiple transcriptomes of the African oil palm (Elaeis guineensis) to identify reference genes for RT-PCR. J Biotechnol. 2014; 184:63–73. pmid:24862192
- 41. Wang NA, Xiang Y, Fang LC, Wang YJ, Xin HP, Li SH. Patterns of gene duplication and their contribution to expansion of gene families in grapevine. Plant Mol Biol Report. 2013; 31:852–861.
- 42. Wang J, Pan C, Wang Y, Ye L, Wu J, Chen L. Genome-wide identification of MAPK, MAPKK, and MAPKKK gene families and transcriptional profiling analysis during development and stress response in cucumber. BMC Genomics. 2015;16:386. pmid:25976104
- 43. Xie Z, Zhang ZL, Zou X, Huang J, Ruas P, Thompson D. Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signalling in aleurone cells. Plant Physiol. 2005;137:176–189. pmid:15618416
- 44. Li H, Guo D, Yang ZP, Tang X, Peng SQ. Genome-wide identification and characterization of WRKY gene family in Hevea brasiliensis. Genome. 2014; 104:14–23.
- 45. Zou CS, Jiang WB, Yu DQ. Male gametophyte-specific WRKY34 transcription factor mediates cold sensitivity of mature pollen in Arabidopsis. J Exp Bot. 2010; 61:3901–3914. pmid:20643804