Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.)

Yuan, Hongmei; Guo, Wendong; Zhao, Lijuan; Yu, Ying; Chen, Si; Lei, Tao; Cheng, Lili; Qing-hua, Kang; Song, Xin; Wu, Jianzhong; Yao, Yubo; Huang, Wengong; Wu, Ying; Liu, Yan; Yang, Xue; Wu, Guangwen

doi:10.1186/s12864-021-07697-w

Cited by 21 publications

(34 citation statements)

References 85 publications

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“…Among them, ClWRKY20 , 21 , and 55 possessed a unique pattern “WNSIVV” which was conserved in these three members. Clustering of one domain WRKY of factors in group I is consistent with the study of the WRKY TF family in Linum usitatissimum ( Yuan et al, 2021 ). The same results are reported in Cicer arietinum ( Kumar et al, 2016 ).…”

Section: Discussionsupporting

confidence: 86%

Characterization of WRKY Gene Family in Whole-Genome and Exploration of Flowering Improvement Genes in Chrysanthemum lavandulifolium

Khan

Kang

et al. 2022

Front. Plant Sci.

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Chrysanthemum is a well-known ornamental plant with numerous uses. WRKY is a large family of transcription factors known for a variety of functions ranging from stress resistance to plant growth and development. Due to the limited research on the WRKY family in chrysanthemums, we examined them for the first time in Chrysanthemum lavandulifolium. A total of 138 ClWRKY genes were identified, which were classified into three groups. Group III in C. lavandulifolium contains 53 members, which is larger than group III of Arabidopsis. The number of introns varied from one to nine in the ClWRKY gene family. The “WRKYGQK” motif is conserved in 118 members, while other members showed slight variations. AuR and GRE responsive cis-acting elements were located in the promoter region of WRKY members, which are important for plant development and flowering induction. In addition, the W box was present in most genes; the recognition site for the WRKY gene may play a role in autoregulation and cross-regulation. The expression of the most variable 19 genes in terms of different parameters was observed at different stages. Among them, 10 genes were selected due to the presence of CpG islands, while nine genes were selected based on their close association with important Arabidopsis genes related to floral traits. ClWRKY36 and ClWRKY45 exhibit differential expression at flowering stages in the capitulum, while methylation is detected in three genes, including ClWRKY31, ClWRKY100, and ClWRKY129. Our results provide a basis for further exploration of WRKY members to find their functions in plant growth and development, especially in flowering traits.

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Section: Discussionsupporting

confidence: 86%

Characterization of WRKY Gene Family in Whole-Genome and Exploration of Flowering Improvement Genes in Chrysanthemum lavandulifolium

Khan

Kang

et al. 2022

Front. Plant Sci.

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“…Compared with some higher angiosperms, the LchiWRKY family has a smaller number. For example, there are 125 ZmWRKY genes in the maize ( Zea mays ) genome [ 43 ], 108 HbWRKY genes in the Rubber Tree ( Hevea brasiliensis ) genome [ 44 ], 102 LuWRKY genes in Flax ( Linum usitatissimum L.) genome [ 45 ], 86 HvWRKY genes in Barley ( Hordeum vulgare L.) genome [ 46 ], and 64 IiWRKY genes were identified in the whole genome of Isatis indigotica [ 47 ]. A total of 61 CsWRKY genes in the Cucumber ( Cucumis sativus L.) genome [ 4 ], 57 CmWRKY genes were identified in the melon ( Cucumis Melo L.) genome [ 48 ], and 54 AcWRKYs in Pineapple ( Ananas comosus (L.) Merr.)…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress

Zhu

et al. 2022

BMC Plant Biol

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Background Liriodendron chinense (Lchi) is a tree species within the Magnoliaceae family and is considered a basal angiosperm. The too low or high temperature or soil drought will restrict its growth as the adverse environmental conditions, thus improving L. chinense abiotic tolerance was the key issues to study. WRKYs are a major family of plant transcription factors known to often be involved in biotic and abiotic stress responses. So far, it is still largely unknown if and how the LchiWRKY gene family is tied to regulating L. chinense stress responses. Therefore, studying the involvement of the WRKY gene family in abiotic stress regulation in L. chinense could be very informative in showing how this tree deals with such stressful conditions. Results In this research, we performed a genome-wide analysis of the Liriodendron chinense (Lchi) WRKY gene family, studying their classification relationships, gene structure, chromosomal locations, gene duplication, cis-element, and response to abiotic stress. The 44 members of the LchiWRKY gene family contain a significant amount of sequence diversity, with their lengths ranging from 525 bp to 40,981 bp. Using classification analysis, we divided the 44 LchiWRKY genes into three phylogenetic groups (I, II, II), with group II then being further divided into five subgroups (IIa, IIb, IIc, IId, IIe). Comparative phylogenetic analysis including the WRKY families from 17 plant species suggested that LchiWRKYs are closely related to the Magnolia Cinnamomum kanehirae WRKY family, and has fewer family members than higher plants. We found the LchiWRKYs to be evenly distributed across 15 chromosomes, with their duplication events suggesting that tandem duplication may have played a major role in LchiWRKY gene expansion model. A Ka/Ks analysis indicated that they mainly underwent purifying selection and distributed in the group IId. Motif analysis showed that LchiWRKYs contained 20 motifs, and different phylogenetic groups contained conserved motif. Gene ontology (GO) analysis showed that LchiWRKYs were mainly enriched in two categories, i.e., biological process and molecular function. Two group IIc members (LchiWRKY10 and LchiWRKY37) contain unique WRKY element sequence variants (WRKYGKK and WRKYGKS). Gene structure analysis showed that most LchiWRKYs possess 3 exons and two different types of introns: the R- and V-type which are both contained within the WRKY domain (WD). Additional promoter cis-element analysis indicated that 12 cis-elements that play different functions in environmental adaptability occur across all LchiWRKY groups. Heat, cold, and drought stress mainly induced the expression of group II and I LchiWRKYs, some of which had undergone gene duplication during evolution, and more than half of which had three exons. LchiWRKY33 mainly responded to cold stress and LchiWRKY25 mainly responded to heat stress, and LchiWRKY18 mainly responded to drought stress, which was almost 4-fold highly expressed, while 5 LchiWRKYs (LchiWRKY5, LchiWRKY23, LchiWRKY14, LchiWRKY27, and LchiWRKY36) responded equally three stresses with more than 6-fold expression. Subcellular localization analysis showed that all LchiWRKYs were localized in the nucleus, and subcellular localization experiments of LchiWRKY18 and 36 also showed that these two transcription factors were expressed in the nucleus. Conclusions This study shows that in Liriodendron chinense, several WRKY genes like LchiWRKY33, LchiWRKY25, and LchiWRKY18, respond to cold or heat or drought stress, suggesting that they may indeed play a role in regulating the tree’s response to such conditions. This information will prove a pivotal role in directing further studies on the function of the LchiWRKY gene family in abiotic stress response and provides a theoretical basis for popularizing afforestation in different regions of China.

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“…With the development of molecular techniques, members of this gene family have been discovered in an increasing number of varied species. 74 WRKYs have been identified in Arabidopsis, 109 in rice [ 32 , 33 ], 104 in poplar [ 34 ], 102 in flax [ 35 ], 45 in Eucommia ulmoides [ 36 ], 57 in melon [ 37 ], 86 in barley [ 38 ], and 64 in Isatis indigotica [ 39 ]. Previous study also revealed 127 WRKY members in apple [ 25 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the WRKY Gene Family in Malus domestica and the Role of MdWRKY70L in Response to Drought and Salt Stresses

Qin

Cheng

et al. 2022

Genes

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The WRKY transcription factors are unique regulatory proteins in plants, which are important in the stress responses of plants. In this study, 113 WRKY genes were identified from the apple genome GDDH13 and a comprehensive analysis was performed, including chromosome mapping, and phylogenetic, motif and collinearity analysis. MdWRKYs are expressed in different tissues, such as seeds, flowers, stems and leaves. We analyzed seven WRKY proteins in different groups and found that all of them were localized in the nucleus. Among the 113 MdWRKYs, MdWRKY70L was induced by both drought and salt stresses. Overexpression of it in transgenic tobacco plants conferred enhanced stress tolerance to drought and salt. The malondialdehyde content and relative electrolyte leakage values were lower, while the chlorophyll content was higher in transgenic plants than in the wild-type under stressed conditions. In conclusion, this study identified the WRKY members in the apple genome GDDH13, and revealed the function of MdWRKY70L in the response to drought and salt stresses.

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Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.)

Cited by 21 publications

References 85 publications

Characterization of WRKY Gene Family in Whole-Genome and Exploration of Flowering Improvement Genes in Chrysanthemum lavandulifolium

Characterization of WRKY Gene Family in Whole-Genome and Exploration of Flowering Improvement Genes in Chrysanthemum lavandulifolium

Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress

Genome-Wide Analysis of the WRKY Gene Family in Malus domestica and the Role of MdWRKY70L in Response to Drought and Salt Stresses

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