Phylogenetic analysis and transcriptional profiling of WRKY genes in sunflower (Helianthus annuus L.): Genetic diversity and their responses to different biotic and abiotic stresses

Liu, Ake; Liu, Cheng‐Lin; Lei, Haiying; Wang, Zhijun; Zhang, Min; Yan, Xi; Yang, Guang; Ren, Jia-Lin

doi:10.1016/j.indcrop.2020.112268

Cited by 28 publications

(29 citation statements)

References 73 publications

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“…Identi cation of the WRKY genes A total of 104 candidate WRKY genes were predicted from H. annuus, among which 14 were removed after domain check and the rest 90 were named as HaWRKY1-HaWRKY90 (Supplementary Table 2). In comparison to the results of Guo et al [20] and Liu et al [21], one gene (HaWRKY51) in our study was found not inculded in the previous works, whereas the rest had their corresponding genes. The length of these genes ranged from 388 bp (HaWRKY5) to 8445 bp (HaWRKY49), with molecular weight (MW) from 10.48 to 74.25 kDa.…”

Section: Resultscontrasting

confidence: 73%

“…2), corresponding to group I, II and III in Arabidopsis [2] and an extra WKKY group. In contrast, Guo et al [20] and Liu et al [21] just distributed genes in this WKKY group into group I, II and III. Among 90 HaWRKY family members, group II accounts for the largest part with 48 HaWRKY proteins, followed by group I with 18 proteins and group III with 17 proteins (Fig.…”

Section: Phylogenetic Analysis Of Wrky Family Membersmentioning

confidence: 88%

“…Systematical characterization of WRKY genes in several species has been studied, including Arabidopsis, rice, tomato, maize etc. Sun ower WRKY genes have been well characterized bene ting from the release of its reference genome in previous studies [20][21]. However, there are two sun ower genome database available ("HanXRQr1.0" and "HA412.v1.1.bronze") assembled from different sun ower genotypes .…”

Section: Discussionmentioning

confidence: 99%

“…However, there are two sun ower genome database available ("HanXRQr1.0" and "HA412.v1.1.bronze") assembled from different sun ower genotypes . Guo et al [20] and Liu et al [21] have used the "HanXRQr1.0" database for retrieval of WRKY genes. In our study, we used "HA412.v1.1.bronze" database to search WRKY genes as support and addition to the previous works.…”

Section: Discussionmentioning

confidence: 99%

“…Badouin et al [19] reported a high-quality reference for the sun ower genome (3.6 gigabases), with 17 chromosomes and 52,232 protein-coding genes on them. Guo et al [20] identify 112 sun ower WRKY genes from this reference genome and Liu et al [21] have extended this family to 119 members. In the current study, another sun ower database from a different sun ower genotype was used to search WRKY genes as support and addition to the previous works.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

Chong

Islam

et al. 2020

Preprint

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Abstract Background: WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. However, the information about WRKY genes in Helianthus annuus L. (common sunflower) is limited. Results: Ninety WRKY (HaWRKY) genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group and HaWRKY genes within same group or subgroup generally showed similar exon-intron structures and motif compositions. The tandem and segmental duplication possibly contributed to the diversity and expansion of HaWRKY gene families. Synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses. Conclusions: Ninety WRKY (HaWRKY) genes were identified from H. annuus L. and classified into four groups. Structures of HaWRKY proteins and their evolutionary characteristics were also investigated. The characterization of HaWRKY genes and their expression profiles under biotic and abiotic stresses in this study provide a foundation for further functional analyses of these genes. Therefore, these functional genes related to increasing the plant tolerance or improving the crop quality, could be applied for the crop improvement..

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Section: Resultscontrasting

confidence: 73%

Section: Phylogenetic Analysis Of Wrky Family Membersmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

Chong

Islam

et al. 2020

Preprint

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Multi-algorithm cooperation research of WRKY genes under nitrogen stress in Panax notoginseng

Zhang

et al. 2022

Protoplasma

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Expansion and adaptive evolution of the WRKY transcription factor family in Avicennia mangrove trees

Feng

et al. 2023

Mar Life Sci Technol

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Mangroves are adapted to intertidal zones, which present extreme environmental conditions. WRKYs are among the most prominent transcription factors (TFs) in higher plants and act through various interconnected networks to regulate responses to multiple abiotic stressors. Here, based on omic data, we investigated the landscape and evolutionary patterns of WRKYs in the main mangrove genus Avicennia. We found that both the number and the proportion of TFs and WRKYs in Avicennia species exceeded their inland relatives, indicating a significant expansion of WRKYs in Avicennia. We identified 109 WRKY genes in the representative species Avicennia marina. Comparative genomic analysis showed that two recent whole-genome duplication (WGD) events played a critical role in the expansion of WRKYs, and 88% of Avicennia marina WRKYs (AmWRKYs) have been retained following these WGDs. Applying comparative transcriptomics on roots under experimental salt gradients, we inferred that there is high divergence in the expression of WGD-retained AmWRKYs. Moreover, we found that the expression of 16 AmWRKYs was stable between freshwater and moderately saline water but increased when the trees were exposed to high salinity. In particular, 14 duplicates were retained following the two recent WGD events, indicating potential neo- and sub-functionalization. We also found that WRKYs could interact with other upregulated genes involved in signalling pathways and natural antioxidant biosynthesis to enhance salt tolerance, contributing to the adaptation to intertidal zones. Our omic data of the WRKY family in A. marina broadens the understanding of how a TF family relates to the adaptive evolution of mangroves.

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Phylogenetic analysis and transcriptional profiling of WRKY genes in sunflower (Helianthus annuus L.): Genetic diversity and their responses to different biotic and abiotic stresses

Cited by 28 publications

References 73 publications

Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

Multi-algorithm cooperation research of WRKY genes under nitrogen stress in Panax notoginseng

Expansion and adaptive evolution of the WRKY transcription factor family in Avicennia mangrove trees

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