Genome-Wide Identification, Evolutionary and Functional Analyses of WRKY Family Members in Ginkgo biloba

Li, Weixing; Xiao, Nan; Wang, Yawen; Liu, Ximeng; Chen, Zhaoyu; Gu, Xiaoyin; Chen, Yadi

doi:10.3390/genes14020343

Cited by 9 publications

(3 citation statements)

References 86 publications

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“…Previous studies have identified variants of the conserved WRKYGQK motif in multiple species. Two variants (WKKYGKK and WKKYGEK) have been reported for Taraxacum kok-saghyz [ 39 ], while Ginkgo biloba has four variants: WRKYAQK, WRKYGEK, WRKYGRK, and WRKYGKK [ 40 ]. Moreover, three variants have been observed in Kandelia obovata (WRKYGEK, WRKYGKK, and WRKYGQK) [ 41 ] and one in Cannabis sativa (WRKYGKK) [ 42 ].…”

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

View full text Add to dashboard Cite

show abstract

“…Previous studies have identi ed variants of the conserved WRKYGQK motif in multiple species. Two variants (WKKYGKK and WKKYGEK) have been reported for Taraxacum kok-saghyz [39], while Ginkgo biloba has four variants: WRKYAQK, WRKYGEK, WRKYGRK, and WRKYGKK [40]. Moreover, three variants have been observed in Kandelia obovata (WRKYGEK, WRKYGKK, and WRKYGQK) [41] and one in Cannabis sativa (WRKYGKK) [42].…”

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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“…Many studies have focused on the tolerance of G. biloba. With the release of the ginkgo genome sequence, more gene families associated with resistance traits in G. biloba are being revealed [15,16]. However, information on the NF-Y family in G. biloba remains scarce.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification, Characterization, and Expression Analysis of NF-Y Gene Family in Ginkgo biloba Seedlings and GbNF-YA6 Involved in Heat-Stress Response and Tolerance

Wang,

Zou,

Ren

et al. 2023

IJMS

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Nuclear factor Y (NF-Y) transcription factors play an essential role in regulating plant growth, development, and stress responses. Despite extensive research on the NF-Y gene family across various species, the knowledge regarding the NF-Y family in Ginkgo biloba remains unknown. In this study, we identified a total of 25 NF-Y genes (seven GbNF-YAs, 12 GbNF-YBs, and six GbNF-YCs) in the G. biloba genome. We characterized the gene structure, conserved motifs, multiple sequence alignments, and phylogenetic relationships with other species (Populus and Arabidopsis). Additionally, we conducted a synteny analysis, which revealed the occurrence of segment duplicated NF-YAs and NF-YBs. The promoters of GbNF-Y genes contained cis-acting elements related to stress response, and miRNA–mRNA analysis showed that some GbNF-YAs with stress-related cis-elements could be targeted by the conserved miRNA169. The expression of GbNF-YA genes responded to drought, salt, and heat treatments, with GbNF-YA6 showing significant upregulation under heat and drought stress. Subcellular localization indicated that GbNF-YA6 was located in both the nucleus and the membrane. Overexpressing GbNF-YA6 in ginkgo callus significantly induced the expression of heat-shock factors (GbHSFs), and overexpressing GbNF-YA6 in transgenic Arabidopsis enhanced its heat tolerance. Additionally, Y2H assays demonstrated that GbNF-YA6 could interact with GbHSP at the protein level. Overall, our findings offer novel insights into the role of GbNF-YA in enhancing abiotic stress tolerance and warrant further functional research of GbNF-Y genes.

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Genome-Wide Identification, Evolutionary and Functional Analyses of WRKY Family Members in Ginkgo biloba

Cited by 9 publications

References 86 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 Identification, Characterization, and Expression Analysis of NF-Y Gene Family in Ginkgo biloba Seedlings and GbNF-YA6 Involved in Heat-Stress Response and Tolerance

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