Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

Mu, Detian; Chen, Wenqiang; Shao, Yingying; Wilson, Iain W.; Zhao, Huan; Luo, Zuliang; Lin, Xiaodong; He, Jialong; Zhang, Yuan; Mo, Changming; Qiu, Deyou; Tang, Qi

doi:10.3390/plants12020288

Cited by 10 publications

(4 citation statements)

References 67 publications

(79 reference statements)

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“…Furthermore, PsWRKY39 is localised in the chloroplast and is speculated to be involved in chloroplast formation, thereby affecting photosynthesis. Phylogenetic analysis based on AtWRKYs divided the 55 PsWRKYs into three groups, with the largest proportion of PsWRKYs in Group II (67%), suggesting that this taxon may have undergone gene duplication events during evolution in Hypericum perforatum [ 34 ], Siraitia siamensis [ 35 ] and P. armeniaca [ 30 ]. Group II was subdivided into five subgroups in which members II-e and II-d were concentrated in two adjacent branches of the same subgroup, as were members of II-a and II-b.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica

et al. 2023

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Background WRKY transcription factors are a prominent gene family in plants, playing a crucial role in various biological processes including development, metabolism, defense, differentiation, and stress response. Although the WRKY gene family has been extensively studied and analysed in numerous plant species, research on Prunus sibirica’s WRKY genes (PsWRKY) remains lacking. Results This study analysed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, and Gene ontology (GO) annotation of PsWRKY gene family members using bioinformatics methods based on the whole-genome data of P. sibirica. In total, 55 WRKYs were identified in P. sibirica and were heterogeneously distributed on eight chromosomes. Based on the phylogenetic analysis, these WRKYs were classified into three major groups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Members of different subfamilies have different cis-acting elements, conserved motifs, and intron-exon structures, indicating functional heterogeneity of the WRKY family. Prediction of subcellular localisation indicated that PsWRKYs were mainly located in the nucleus. Twenty pairs of duplicated genes were identified, and segmental duplication events may play an important role in PsWRKY gene family expansion. Analysis of the Ka/Ks ratio showed that the PsWRKY family’s homologous genes were primarily purified by selection. Additionally, GO annotation analysis showed that the WRKY gene family was mainly involved in responses to stimuli, immune system processes, and reproductive processes. Furthermore, quantitative real-time PCR (qRT-PCR) analysis showed that 23 PsWRKYs were highly expressed in one or more tissues (pistils and roots) and PsWRKYs showed specific expression patterns under different low-temperature stress conditions. Conclusions Our results provide a scientific basis for the further exploration and functional validation of WRKYs in P. sibirica.

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica

et al. 2023

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“…Furthermore, PsWRKY39 is localised in the chloroplast and is speculated to be involved in chloroplast formation, thereby affecting photosynthesis. Phylogenetic analysis based on AtWRKYs divided the 55 PsWRKYs into three groups, with the largest proportion of PsWRKYs in Group II (67%), suggesting that this taxon may have undergone gene duplication events during evolution in Hypericum perforatum [34], Siraitia siamensis [35] and P. armeniaca [30]. Group II was subdivided into ve subgroups in which members II-e and II-d were concentrated in two adjacent branches of the same subgroup, as were members of II-a and II-b.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica

Liu

Wang

Wen

et al. 2023

Preprint

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Background: WRKY transcription factors are a prominent gene family in plants, playing a crucial role in various biological processes including development, metabolism, defense, differentiation, and stress response. Although the WRKY gene family has been extensively studied and analysed in numerous plant species, research on Prunus sibirica's WRKYgenes (PsWRKY) remains lacking. Results: This study analysed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, and Gene ontology (GO) annotation of PsWRKY gene family members using bioinformatics methods based on the whole-genome data of P. sibirica. In total, 55 WRKYswere identified in P. sibirica and were heterogeneously distributed on eight chromosomes. Based on the phylogenetic analysis, these WRKYs were classified into three major groups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Members of different subfamilies have different cis-acting elements, conserved motifs, and intron-exon structures, indicating functional heterogeneity of the WRKY family. Prediction of subcellular localisation indicated that PsWRKYs were mainly located in the nucleus. Twenty pairs of duplicated genes were identified, and segmental duplication events may play an important role in PsWRKY gene family expansion. Analysis of the Ka/Ks ratio showed that the PsWRKY family's homologous genes were primarily purified by selection. Additionally, GO annotation analysis showed that the WRKY gene family was mainly involved in responses to stimuli, immune system processes, and reproductive processes. Furthermore, quantitative real-time PCR (qRT-PCR) analysis showed that 23 PsWRKYswere highly expressed in one or more tissues (pistils and roots) and PsWRKYs showed specific expression patterns under different low-temperature stress conditions. Conclusions: Our results provide a scientific basis for the further exploration and functional validation of WRKYs in P. sibirica.

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“…The primers used for qRT-PCR Specific primer pairs designed using Beacon Designer 7.0 software are listed in Supplementary Table S3 ; the primers of key enzyme genes involved in TIA biosynthesis pathway have been reported previously with the SAM gene as the internal reference gene [ 62 ]. The qRT-PCR was performed using 2× SYBR Green Pro Taq HS premix (Vazyme, Shanghai, China) and reaction system and procedure have been previously reported [ 63 ], using the following protocol: 95 °C for 3.00 min, 1 cycle; 95 °C for 15 s and 60 °C for 30 s, 40 cycles. The 2 −ΔΔCt method with three replications was performed for analysis and the statistical tests were performed using GraphPad Prism 9.0 software.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Mining of CULLIN E3 Ubiquitin Ligase Genes from Uncaria rhynchophylla

Shao,

Mu,

Zhou

et al. 2024

Plants

Self Cite

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CULLIN (CUL) protein is a subtype of E3 ubiquitin ligase that is involved in a variety of biological processes and responses to stress in plants. In Uncaria rhynchophylla, the CUL gene family has not been identified and its role in plant development, stress response and secondary metabolite synthesis has not been studied. In this study, 12 UrCUL gene members all contained the typical N-terminal domain and C-terminal domain identified from the U. rhynchophylla genome and were classified into four subfamilies based on the phylogenetic relationship with CULs in Arabidopsis thaliana. They were unevenly distributed on eight chromosomes but had a similar structural composition in the same subfamily, indicating that they were relatively conserved and potentially had similar gene functions. An interspecific and intraspecific collinearity analysis showed that fragment duplication played an important role in the evolution of the CUL gene family. The analysis of the cis-acting elements suggests that the UrCULs may play an important role in various biological processes, including the abscisic acid (ABA) response. To investigate this hypothesis, we treated the roots of U. rhynchophylla tissue-cultured seedlings with ABA. The expression pattern analysis showed that all the UrCUL genes were widely expressed in roots with various expression patterns. The co-expression association analysis of the UrCULs and key enzyme genes in the terpenoid indole alkaloid (TIA) synthesis pathway revealed the complex expression patterns of 12 UrCUL genes and some key TIA enzyme genes, especially UrCUL1, UrCUL1-likeA, UrCUL2-likeA and UrCUL2-likeB, which might be involved in the biosynthesis of TIAs. The results showed that the UrCULs were involved in the response to ABA hormones, providing important information for elucidating the function of UrCULs in U. rhynchophylla. The mining of UrCULs in the whole genome of U. rhynchophylla provided new information for understanding the CUL gene and its function in plant secondary metabolites, growth and development.

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Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

Cited by 10 publications

References 67 publications

Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica

Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica

Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica

Genome-Wide Mining of CULLIN E3 Ubiquitin Ligase Genes from Uncaria rhynchophylla

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