Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum

Wu, Zhao-Ming; Shen, Shenghai; Wang, Yueduo; Tao, Weiqi; Zhao, Ziqi; Hu, Xiangli; Yu, Pei

doi:10.3390/plants11192511

Cited by 7 publications

(8 citation statements)

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“…The C2H2-zinc finger protein family plays several important roles in plant growth and development, and has been extensively studied in various species including Arabidopsis thaliana Frontiers in Genetics frontiersin.org (Englbrecht et al, 2004), Zea mays (Wei et al, 2016), Triticum aestivum (Li et al, 2021;Wu et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of the C2H2-zinc finger transcription factor gene family and screening of candidate genes involved in floral development in Coptis teeta Wall. (Ranunculaceae)

Duan,

Zhao,

et al. 2024

Front. Genet.

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Background: C2H2-zinc finger transcription factors comprise one of the largest and most diverse gene superfamilies and are involved in the transcriptional regulation of flowering. Although a large number of C2H2 zinc-finger proteins (C2H2-ZFPs) have been well characterized in a number of model plant species, little is known about their expression and function in Coptis teeta. C. teeta displays two floral phenotypes (herkogamy phenotypes). It has been proposed that the C2H2-zinc finger transcription factor family may play a crucial role in the formation of floral development and herkogamy observed in C. teeta. As such, we performed a genome-wide analysis of the C2H2-ZFP gene family in C. teeta.Results: The complexity and diversity of C. teeta C2H2 zinc finger proteins were established by evaluation of their physicochemical properties, phylogenetic relationships, exon-intron structure, and conserved motifs. Chromosome localization showed that 95 members of the C2H2 zinc-finger genes were unevenly distributed across the nine chromosomes of C. teeta, and that these genes were replicated in tandem and segmentally and had undergone purifying selection. Analysis of cis-acting regulatory elements revealed a possible involvement of C2H2 zinc-finger proteins in the regulation of phytohormones. Transcriptome data was then used to compare the expression levels of these genes during the growth and development of the two floral phenotypes (F-type and M-type). These data demonstrate that in groups A and B, the expression levels of 23 genes were higher in F-type flowers, while 15 genes showed higher expressions in M-type flowers. qRT-PCR analysis further revealed that the relative expression was highly consistent with the transcriptome data.Conclusion: These data provide a solid basis for further in-depth studies of the C2H2 zinc finger transcription factor gene family in this species and provide preliminary information on which to base further research into the role of the C2H2 ZFPs gene family in floral development in C. teeta.

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of the C2H2-zinc finger transcription factor gene family and screening of candidate genes involved in floral development in Coptis teeta Wall. (Ranunculaceae)

Duan,

Zhao,

et al. 2024

Front. Genet.

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“…C2H2-ZFPs are one of the most important transcription factor families in higher plants, playing a crucial role in plant development and stress resistance ( Han et al., 2021 ; Liu et al., 2022a ; Liu et al., 2022b ). Previous reports have shown that they can play important roles in Arabidopsis thaliana , wheat, grapevine, sorghum, and cotton ( Englbrecht et al., 2004 ; Salih et al., 2019 ; Arrey-Salas et al., 2021 ; Cui et al., 2022 ; Wu et al., 2022 ). However, there are few reports on the C2H2-ZFPs in sweetpotato.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of the C2H2 zinc finger gene family and expression analysis under salt stress in sweetpotato

Du,

Zhou,

Qin

et al. 2023

Front. Plant Sci.

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IntroductionThe higher plant transcription factor C2H2 zinc finger protein (C2H2-ZFP) is essential for plant growth, development, and stress response. There are limited studies on C2H2-ZFP genes in sweetpotato, despite a substantial number of C2H2-ZFP genes having been systematically found in plants.MethodsIn this work, 178 C2H2-ZFP genes were found in sweetpotato, distributed randomly on 15 chromosomes, and given new names according to where they were located. These members of the zinc finger gene family are separated into six branches, as shown by the phylogenetic tree. 24 tandem repeats of IbZFP genes and 46 fragment repeats were identified, and a homology study revealed that IbZFP genes linked more regions with wild relative species of sweetpotato as well as rhizome plants like potato and cassava. And we analyzed the expression patterns of IbZFP genes during the early development of sweetpotato storage roots (SRs) and salt stress using transcriptome data, and identified 44 IbZFP genes that exhibited differences in expression levels during the early expansion of sweetpotato SRs in different varieties, and 92 IbZFP genes that exhibited differences in expression levels under salt stress in salt tolerant and salt sensitive sweetpotato varieties. Additionally, we cloned six IbZFP genes in sweetpotato and analyzed their expression patterns in different tissues, their expression patterns under abiotic stress and hormone treatment, and subcellular localization.Results and discussionThe results showed that the IbZFP genes had tissue specificity in sweetpotato and were induced to varying degrees by drought and salt stress. ABA and GA3 treatments also affected the expression of the IbZFP genes. We selected IbZFP105, which showed significant differences in expression levels under salt stress and ABA treatment, to be heterologously expressed in Arabidopsis thaliana. We found that IbZFP105 OE lines exhibited higher tolerance to salt stress and ABA stress. This indicates that IbZFP105 can enhance the salt tolerance of plants. These results systematically identified the evolution and expression patterns of members of the C2H2-ZFP gene family in sweetpotato, providing a theoretical basis for studying the role of IbZFP genes in the development of sweetpotato SRs and in resistance to stress.

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“…We evaluated the values of Ks (synonymous) and Ka (nonsynonymous) as well as the ratio of Ka/Ks. Ka/Ks < 1, Ka/Ks = 1, and Ka/Ks > 1 generally indicate negative, neutral, and positive selection, respectively [ 76 , 77 , 78 ].…”

Section: Methodsmentioning

confidence: 99%

Caffeic Acid O-Methyltransferase Gene Family in Mango (Mangifera indica L.) with Transcriptional Analysis under Biotic and Abiotic Stresses and the Role of MiCOMT1 in Salt Tolerance

Wang,

Chen,

Luo

et al. 2024

IJMS

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Caffeic acid O-methyltransferase (COMT) participates in various physiological activities in plants, such as positive responses to abiotic stresses and the signal transduction of phytohormones. In this study, 18 COMT genes were identified in the chromosome-level reference genome of mango, named MiCOMTs. A phylogenetic tree containing nine groups (I-IX) was constructed based on the amino acid sequences of the 71 COMT proteins from seven species. The phylogenetic tree indicated that the members of the MiCOMTs could be divided into four groups. Quantitative real-time PCR showed that all MiCOMT genes have particularly high expression levels during flowering. The expression levels of MiCOMTs were different under abiotic and biotic stresses, including salt and stimulated drought stresses, ABA and SA treatment, as well as Xanthomonas campestris pv. mangiferaeindicae and Colletotrichum gloeosporioides infection, respectively. Among them, the expression level of MiCOMT1 was significantly up-regulated at 6–72 h after salt and stimulated drought stresses. The results of gene function analysis via the transient overexpression of the MiCOMT1 gene in Nicotiana benthamiana showed that the MiCOMT1 gene can promote the accumulation of ABA and MeJA, and improve the salt tolerance of mango. These results are beneficial to future researchers aiming to understand the biological functions and molecular mechanisms of MiCOMT genes.

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Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum

Cited by 7 publications

References 95 publications

Genome-wide identification and expression analysis of the C2H2-zinc finger transcription factor gene family and screening of candidate genes involved in floral development in Coptis teeta Wall. (Ranunculaceae)

Genome-wide identification and expression analysis of the C2H2-zinc finger transcription factor gene family and screening of candidate genes involved in floral development in Coptis teeta Wall. (Ranunculaceae)

Genome-wide identification of the C2H2 zinc finger gene family and expression analysis under salt stress in sweetpotato

Caffeic Acid O-Methyltransferase Gene Family in Mango (Mangifera indica L.) with Transcriptional Analysis under Biotic and Abiotic Stresses and the Role of MiCOMT1 in Salt Tolerance

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