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Unrooted phylogenetic tree representing the relationships among 163 AP2/ERF protein of ginger and Arabidopsis. The different colored arcs indicate different groups of the AP2/ERF family. AP2/ERF proteins from ginger with the prefix “Zo” indicate “Zingiber officinale”
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Background
AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally ch...
Similar publications
Nuclear factor Y (NF-Y) plays a vital role in numerous biological processes as well as responses to biotic and abiotic stresses, its function in ginger ( Zingiber officinale Roscoe), a significant medicinal and dietary vegetable, remains largely unexplored. While the NF-Y family has been thoroughly identified in many plant species, and the function...
Citations
... The number of AP2/ERF TFs varies greatly among species. Thus, for example, Zingiber o cinale Roscoe shows163 [27], Triticum aestivum, 322 [28], Fagopyrum tataricum, 134 [29], and A. thaliana, 122. The number of AP2/ERF genes was signi cantly higher in herbaceous plants than in P. sibirica, whereas the number of AP2/ERF genes in woody plants was similar to that of P. sibirica (112), Citrus rootstock (119), and Chinese jujube (119); hence, we hypothesized that AP2/ERF genes in most woody plants are fewer than those in herbaceous plants, presumably owing to the slower evolution of woody plants. ...
Background AP2/ERF transcription factors (TFs) are plant-specific transcription factors involved in the regulation of plant growth and development and in response to stresses. Although AP2/ERF TFs have been identified in numerous species and analyzed in many, such as Oryza sativa, Arabidopsis thaliana, and Populus trichocarpa, studies on the Prunus sibirica AP2/ERF (PsAP2/ERF) gene family have not been reported. In the study, 112 PsAP2/ERFs were identified and categorized into 16 subfamilies.
Results The same subfamilies of PsAP2/ERFs typically exhibited similar exon-intron structures and motif compositions. In all, 50 pairs of segmentally duplicated genes were identified within the PsAP2/ERF gene family. The results showed that 20 PsAP2/ERFswere highly expressed in leaves, roots, and pistils, and highly expressed under different conditions of low temperature stress.
Conclusions This study provides a solid scientific foundation for follow-up research on the evolutionary characteristics of AP2/ERFs in P. sibirica, leading to an improved understanding of the molecular basis of their developmental and low-temperature stress responses, and further investigating the functional expression of PsAP2/ERFs.
... The rhizome of ginger, a revered culinary spice and a staple in dietary supplements, boasts a rich composition of essential amino acids, minerals, vitamins, dietary fibers, and flavonoids [4]. The development of the ginger rhizome is a delicately regulated biological process, underpinned by a suite of genes pivotal to its morphogenesis and maturation [5]. Moreover, with the release of the ginger genome sequence [6], has spurred explorations into transcription factor (TF) families, such as AP2/ERF and GRAS, posited to influence rhizome ontogeny [5,7]. ...
... The development of the ginger rhizome is a delicately regulated biological process, underpinned by a suite of genes pivotal to its morphogenesis and maturation [5]. Moreover, with the release of the ginger genome sequence [6], has spurred explorations into transcription factor (TF) families, such as AP2/ERF and GRAS, posited to influence rhizome ontogeny [5,7]. Despite these advances, such factors constitute but a fraction of the elaborate transcriptional network governing rhizome development in ginger. ...
Background
Zingiber officinale Roscoe, colloquially known as ginger, is a crop of significant medicinal and culinary value that frequently encounters adversity stemming from inhospitable environmental conditions. The MYB transcription factors have garnered recognition for their pivotal role in orchestrating a multitude of plant biological pathways. Nevertheless, the enumeration and characterization of the MYBs within Z. officinale Roscoe remains unknown. This study embarks on a genome-wide scrutiny of the MYB gene lineage in ginger, with the aim of cataloging all ZoMYB genes implicated in the biosynthesis of gingerols and curcuminoids, and elucidating their potential regulatory mechanisms in counteracting abiotic stress, thereby influencing ginger growth and development.
Results
In this study, we identified an MYB gene family comprising 231 members in ginger genome. This ensemble comprises 74 singular-repeat MYBs (1R-MYB), 156 double-repeat MYBs (R2R3-MYB), and a solitary triple-repeat MYB (R1R2R3-MYB). Moreover, a comprehensive analysis encompassing the sequence features, conserved protein motifs, phylogenetic relationships, chromosome location, and gene duplication events of the ZoMYBs was conducted. We classified ZoMYBs into 37 groups, congruent with the number of conserved domains and gene structure analysis. Additionally, the expression profiles of ZoMYBs during development and under various stresses, including ABA, cold, drought, heat, and salt, were investigated in ginger utilizing both RNA-seq data and qRT-PCR analysis.
Conclusion
This work provides a comprehensive understanding of the MYB family in ginger and lays the foundation for the future investigation of the potential functions of ZoMYB genes in ginger growth, development and abiotic stress tolerance of ginger.
... Ginger can withstand a certain degree of drought; however, long-term drought has a significant inhibitory effect on rhizome growth, resulting in reduced yields. Ginger seedlings often suffer from severe salt damage [28]. To breed new varieties, it is necessary to investigate the developmental mechanisms and abiotic tolerance of ginger. ...
... Environmental factors strongly influence the distribution and growth of ginger [28]. Therefore, developing highly resistant ginger varieties that can withstand various adversities is a crucial aspect of the advancement for ginger cultivation industry. ...
... AP2/ERF transcription factors are involved in various environmental stress response processes, including cold, heat, drought, and salinity [58,59]. Research indicates that the ZoAP2 genes have a significant impact on ginger growth and development [28]. While, ZoPP2Cs were found to have different AP2/ERF binding sites, which may have a combined function in regulating both adversity and growth/development, but further investigation is needed. ...
Background
Protein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published.
Results
In this study, 97 ZoPP2C genes were identified based on the ginger genome. These genes were classified into 15 branches (A-O) according to the phylogenetic analysis and distributed unevenly on 11 ginger chromosomes. The proteins mainly functioned in the nucleus. Similar motif patterns and exon/intron arrangement structures were identified in the same subfamily of ZoPP2Cs. Collinearity analysis indicated that ZoPP2Cs had 33 pairs of fragment duplicated events uniformly distributed on the corresponding chromosomes. Furthermore, ZoPP2Cs showed greater evolutionary proximity to banana’s PP2Cs. The forecast of cis-regulatory elements and transcription factor binding sites demonstrated that ZoPP2Cs participate in ginger growth, development, and responses to hormones and stresses. ZoERFs have plenty of binding sites of ZoPP2Cs, suggesting a potential synergistic contribution between ZoERFs and ZoPP2Cs towards regulating growth/development and adverse conditions. The protein–protein interaction network displayed that five ZoPP2Cs (9/23/26/49/92) proteins have robust interaction relationship and potential function as hub proteins. Furthermore, the RNA-Seq and qRT-PCR analyses have shown that ZoPP2Cs exhibit various expression patterns during ginger maturation and responses to environmental stresses such as chilling, drought, flooding, salt, and Fusarium solani. Notably, exogenous application of melatonin led to notable up-regulation of ZoPP2Cs (17/59/11/72/43) under chilling stress.
Conclusions
Taken together, our investigation provides significant insights of the ginger PP2C gene family and establishes the groundwork for its functional validation and genetic engineering applications.
... The expression level of ZoDUF668s (Fragments Per Kilobase of exon model per million mapped fragments) was calculated by Cufflinks. Log 2 (FPKM + 1) values and R package "pheatmap" (R-4.2.2) were used to generate the heatmap to illustrate the expression profiling of ZoDUF668s under various growth stages and stress conditions [33]. ...
The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger by the bioinformatics method and unevenly distributed on six chromosomes. Conserved domain analysis showed that members of the same subfamily had similar conserved motifs and gene structures. The promoter region of ZoDUF668s contained the light, plant hormone and stress-responsive elements. The prediction of miRNA targeting relationship showed that nine ginger miRNAs targeted four ZoDUF668 genes through cleavage. The expression patterns of 12 ZoDUF668 genes under biotic and abiotic stress were analyzed using RT-qPCR. The results showed that the expression of seven ZoDUF668 genes was significantly downregulated under Fusarium solani infection, six ZoDUF668 genes were upregulated under cold stress, and five ZoDUF668 genes were upregulated under waterlogging stress. These results indicate that the ZoDUF668 gene has different expression patterns under different stress conditions. This study provides excellent candidate genes and provides a reference for stress-resistance research in ginger.
... Thus, a theoretical foundation was established to harness the great potential of these compounds for industrial application. Given the extensive research of the plant genome, members of the AP2/ERF gene family have been identified in Raphanus sativus (Karanja et al., 2019), Zingiber officinale (Xing et al., 2021), Arachis hypogaea , Oryza sativa (Sharoni et al., 2011), Saccharum officinarum (P. Li et al., 2020), Zea mays (J. ...
Terpenoids are the main active components in the Zanthoxylum armatum leaves, which have extensive medicinal value. The Z. armatum leaf is the main by‐product in the Z. armatum industry. However, the transcription factors involved in the biosynthesis of terpenoids are rarely reported. This study was performed to identify and classify the APETALA2/ethylene‐responsive factor (AP2/ERF) gene family of Z. armatum. The chromosome distribution, gene structure, conserved motifs, and cis‐acting elements of the promoter of the species were also comprehensively analyzed. A total of 214 ZaAP2/ERFs were identified. From the obtained transcriptome and terpenoid content data, four candidate ZaAP2/ERFs involved in the biosynthesis of terpenoids were selected via correlation and weighted gene co‐expression network analysis. A phylogenetic tree was constructed using 13 AP2/ERFs related to the biosynthesis of terpenoids in other plants. ZaERF063 and ZaERF166 showed close evolutionary relationships with the ERFs in other plant species and shared a high AP2‐domain sequence similarity with the two closest AP2/ERF proteins, namelySmERF8 from Salvia miltiorrhiza and AaERF4 from Artemisia annua. Further investigation into the effects of methyl jasmonate (MeJA) treatment on the content of terpenoids in Z. armatum leaves revealed that MeJA significantly induced the upregulation of ZaERF166 and led to a significant increase in the terpenoids content in Z. armatum leaves, indicating that ZaERF166 might be involved in the accumulation of terpenoids of Z. armatum. Results will be beneficial for the functional characterization of AP2/ERFs in Z. armatum and establishment of the theoretical foundation to increase the production of terpenoids via the manipulation of the regulatory elements and strengthen the development and utilization of Z. armatum leaves.
... It results in the existence of repeated chromosomal blocks in the genome. Tandem duplications are groups of two or more members of the same gene family located next to each other on the same chromosome(Cannon, et al. 2004;Xing, et al. 2021). To better understand gene duplication events in chickpea, ...
Harsh environments continuously impact the growth and development of plants, leading to reduced productivity. Therefore, it is crucial to study the acclimation processes to understand the underlying mechanisms for developing climate-resilient plants. Chickpea ( Cicer arietinum L.) is a leguminous crop known for its high protein and carbohydrate content. Though the crop is grown in arid and semi-arid regions, they are vulnerable to extreme stress conditions such as drought stress. Studies on drought-responsive genes were therefore necessary on important economical crop plant like chickpea. The filamentous temperature-sensitive protease H ( ftsH ) family is speculated to play roles in drought stress response. FtsH protease is a membrane-anchored, zinc metalloprotease, belonging to AAA protease family restricted to organelles of endo-symbiotic origin. FtsH is a critical gene for plant chloroplast development and its photosynthetic control. In our present study, we have identified fourteen FtsH protease-encoding genes providing a comprehensive analysis of the Ca-FtsH gene family. The structure and organization of FtsH genes and their corresponding proteins were studied using different in-silico tools and expression profiling was performed through qRT-PCR. The CaFtsH genes play a crucial role in plant growth and development under abiotic stress, revealed by their differential expression pattern during different stress conditions. The gene expression provided a basis for the functional analysis for the stress-responsive ABA signal transduction pathways. These findings contribute to a better understanding of the biological significance of the FtsH genes and requires further characterization to dissect the precise role of these genes.
... org/) . Then, the pecan bZIP family protein sequences were obtained through BLASTp searching against the genome database of C. illinoinensis using the known sequences of A. thaliana, setting an e-value of ≤ − 10 and a score of ≥ 100 (Xing et al. 2021). To more accurately obtain the pecan bZIP, the returned protein sequence was further screened by HMM to obtain the registration number PF00170.22 (BZIP_1. ...
The basic leucine zipper (bZIP) is a transcription factor broadly found in higher plants and is involved in numerous crucial physiological processes: growth and development, stress responses, etc. The pecan (Carya illinoinensis) is a highly ornamental and economical woody plant that is popular in landscape and economic forestry. However, the identification and analysis of the bZIP TF system in pecan have not been reported. To acquire information on the bZIP gene family in pecan, we appraised 77 members of the bZIP gene family from the pecan genome and categorized them into 12 subfamilies (S, B, A, D, F, E, G, I, J, H, K, and C) using bioinformatics methods. Analysis in terms of gene structure and conserved motif composition revealed that each subtribe shares a comparable number of introns-exons and functions. Ka/Ks results suggested that bZIP evolution was influenced by purifying selection. The promoter cis-acting element analysis revealed a huge number of abscisic acid–responsive elements, light-responsive elements, and jasmonic acid–responsive elements in pecan bZIPs. Furthermore, the protein interaction network predicted a possible role for S1-bZIPs in abiotic stress, and the qRT-PCR results further demonstrated that this subpopulation responds to abiotic stress. Meanwhile, the results of subcellular localization and transcriptional activity indicated that CibZIP38, CibZIP55, and CibZIP43 are all nuclear-localized transcriptional activators. The report of the pecan bZIP gene family in this work can further improve our understanding of CibZIPs as a genetic resource for the genetic engineering breeding of pecan.
... These events serve as crucial driving factors for the functional diversity and evolution of gene families [45][46][47]. These findings align with those observed in Arabidopsis and rice, suggesting a similar replication pattern for the TCP gene family in plant genomes [48]. Furthermore, studies have indicated that repetitive genes are expressed in different tissues or organs, implying that these repetitive genes possess specific or redundant cellular functions throughout ginger's growth and development [49]. ...
Ginger (Zingiber officinale Roscoe), a widely consumed edible and medicinal plant, possesses significant nutritional and economic value. Abiotic stresses such as drought and low temperatures can impact the growth and development of ginger. The plant-specific transcription factor Teosinte branched1/cycloidea/proliferating cell factor (TCP) has progressively been identified in various plants for its role in regulating plant growth and development as well as conferring resistance to abiotic stresses. However, limited information on the TCP family is available in ginger. In this study, we identified 20 TCP members in the ginger genome, which were randomly distributed across 9 chromosomes. Based on phylogenetic analysis, these ginger TCP were classified into two subfamilies: Class I (PCF) and Class II (CIN, CYC/TB). The classification of the identified ginger TCPs was supported by a multi-species phylogenetic tree and motif structure analysis, suggesting that the amplification of the ginger TCP gene family occurred prior to the differentiation of angiosperms. The promoter region of ginger TCP genes was found to contain numerous cis-acting elements associated with plant growth, development, and abiotic stress response. Among these elements, the stress response element, anaerobic induction, and MYB binding site play a dominant role in drought responsiveness. Additionally, expression pattern analysis revealed variations in the expression of ginger TCP gene among different tissues and in response to diverse abiotic stresses (drought, low temperature, heat, and salt). Our research offers a thorough examination of TCP members within the ginger plant. This analysis greatly contributes to the understanding of how TCP genes regulate tissue development and response to stress, opening up new avenues for further exploration in this field.
... The specific or redundant cellular functions of these genes during the development of other plants have been observed [47]. Subsequent investigations revealed that the motif positions and compositions of these genes were identical, suggesting that differential gene expression may be attributed to gene mutations that occurred during gene duplication, leading to the loss of certain gene segments [48]. Furthermore, changes in the motif composition during the process of gene replication may also contribute to functional differences [49]. ...
Ginger is a valuable crop known for its nutritional, seasoning, and health benefits. However, abiotic stresses, such as high temperature and drought, can adversely affect its growth and development. Heat shock transcription factors (HSFs) have been recognized as crucial elements for enhancing heat and drought resistance in plants. Nevertheless, no previous study has investigated the HSF gene family in ginger. In this research, a total of 25 ZoHSF members were identified in the ginger genome, which were unevenly distributed across ten chromosomes. The ZoHSF members were divided into three groups (HSFA, HSFB, and HSFC) based on their gene structure, protein motifs, and phylogenetic relationships with Arabidopsis. Interestingly, we found more collinear gene pairs between ZoHSF and HSF genes from monocots, such as rice, wheat, and banana, than dicots like Arabidopsis thaliana. Additionally, we identified 12 ZoHSF genes that likely arose from duplication events. Promoter analysis revealed that the hormone response elements (MEJA-responsiveness and abscisic acid responsiveness) were dominant among the various cis-elements related to the abiotic stress response in ZoHSF promoters. Expression pattern analysis confirmed differential expression of ZoHSF members across different tissues, with most showing responsiveness to heat and drought stress. This study lays the foundation for further investigations into the functional role of ZoHSFs in regulating abiotic stress responses in ginger.
... In Po-VOC-exposed ginger plants, the upregulated genes annotated with the Pfam database for AP2 (PF00847) could be involved in priming ginger plants for resistance to abiotic stresses. Previously, ginger genes annotated with the AP2 domain were upregulated under abiotic stresses (71). ...
The oomycete Pythium oligandrum is a potential biocontrol agent to control a wide range of fungal and oomycete-caused diseases, such as Pythium myriotylum-caused rhizome rot in ginger, leading to reduced yields and compromised quality. Previously, P. oligandrum has been studied for its plant growth-promoting potential by auxin production and induction of disease resistance by elicitors such as oligandrin. Volatile organic compounds (VOCs) play beneficial roles in sustainable agriculture by enhancing plant growth and resistance. We investigated the contribution of P. oligandrum-produced VOCs on plant growth and disease suppression by initially using Nicotiana benthamiana plants for screening. P. oligandrum VOCs significantly enhanced tobacco seedling and plant biomass contents. Screening of the individual VOCs showed that 3-octanone and hexadecane promoted the growth of tobacco seedlings. The total VOCs from P. oligandrum also enhanced the shoot and root growth of ginger plants. Transcriptomic analysis showed a higher expression of genes related to plant growth hormones and stress responses in the leaves of ginger plants exposed to P. oligandrum VOCs. The concentrations of plant growth hormones such as auxin, zeatin, and gibberellic acid were higher in the leaves of ginger plants exposed to P. oligandrum VOCs. In a ginger disease biocontrol assay, the VOC-exposed ginger plants infected with P. myriotylum had lower levels of disease severity. We conclude that this study contributes to understanding the growth-promoting mechanisms of P. oligandrum on ginger and tobacco, priming of ginger plants against various stresses, and the mechanisms of action of P. oligandrum as a biocontrol agent. IMPORTANCE Plant growth promotion plays a vital role in enhancing production of agricultural crops, and Pythium oligandrum is known for its plant growth-promoting potential through production of auxins and induction of resistance by elicitors. This study highlights the significance of P. oligandrum-produced VOCs in plant growth promotion and disease resistance. Transcriptomic analyses of leaves of ginger plants exposed to P. oligandrum VOCs revealed the upregulation of genes involved in plant growth hormone signaling and stress responses. Moreover, the concentration of growth hormones significantly increased in P. oligandrum VOC-exposed ginger plants. Additionally, the disease severity was reduced in P. myriotylum-infected ginger plants exposed to P. oligandrum VOCs. In ginger, P. myriotylum-caused rhizome rot disease results in severe losses, and biocontrol has a role as part of an integrated pest management strategy for rhizome rot disease. Overall, growth enhancement and disease reduction in plants exposed to P. oligandrum-produced VOCs contribute to its role as a biocontrol agent.
