Cis-element Analysis Research Articles

Genome-Wide Identification, Characterization, Evolutionary Analysis, and Expression Pattern of the GPAT Gene Family in Barley and Functional Analysis of HvGPAT18 under Abiotic Stress.

Glycerol-3-phosphoacyltransferase (GPAT) is an important rate-limiting enzyme in the biosynthesis of triacylglycerol (TAG), which is of great significance for plant growth, development, and response to abiotic stress. Although the characteristics of GPAT have been studied in many model plants, little is known about its expression profile and function in barley, especially under abiotic stress. In this study, 22 GPAT genes were identified in the barley genome and divided into three groups (I, II, III), with the latter Group III subdivided further into three subgroups based on the phylogenetic analysis. The analyses of conserved motifs, gene structures, and the three-dimensional structure of HvGPAT proteins also support this classification. Through evolutionary analysis, we determined that HvGPATs in Group I were the earliest to diverge during 268.65 MYA, and the differentiation of other HvGPATs emerged during 86.83-169.84 MYA. The tissue expression profile showed that 22 HvGPAT genes were almost not expressed in INF1 (inflorescence 1). Many functional elements related to stress responses and hormones in cis-element analysis, as well as qRT-PCR results, confirm that these HvGPAT genes were involved in abiotic stress responses. The expression level of HvGPAT18 was significantly increased under abiotic stress and its subcellular localization indicated its function in the endoplasmic reticulum. Various physiological traits under abiotic stress were evaluated using transgenic Arabidopsis to gain further insight into the role of HvGPAT18, and it was found that transgenic seedlings have stronger resistance under abiotic stress than to the wild-type (WT) plants. Overall, our results provide new insights into the evolution and function of the barley GPAT gene family and enable us to explore the molecular mechanism of functional diversity behind the evolutionary history of these genes.

Identification and expression analysis of the GLK gene family in tea plant (Camellia sinensis) and a functional study of CsGLK54 under low-temperature stress

The Golden2-like (GLK) transcription factor family is a significant group of transcription factors in plantae. The currently available studies have shown that GLK transcription factors have been studied mainly in chloroplast growth and development, with fewer studies in abiotic stress regulation. In this study, all tea plant GLK transcription factors were identified for the first time in tea plants, and genome-wide identification, phylogenetic analysis, and thematic characterization were performed to identify 66 GLK transcription factors in tea plants. These genes are categorized into seven groups, and an amino acid sequence comparison analysis is performed. This study revealed that the structure of GLK genes in tea plants is highly conserved and that these genes are distributed across 14 chromosomes. Collinearity analysis revealed 17 pairs of genes with fragment duplications and one pair of genes with tandem duplications, and the analysis of Ka/Ks ratios indicated that most of the genes underwent negative purifying selection. Analysis of promoter cis-elements revealed that the promoters of tea plant GLK genes contain a large number of cis-acting elements related to phytohormones and stress tolerance. In addition, a large number of genes contain LTR elements, suggesting that tea plant GLK genes are involved in low-temperature stress. qRT‒PCR analysis revealed that the expression of CsGLK17, CsGLK38, CsGLK54, CsGLK11 and CsGLK60 significantly increased and that the expression of CsGLK7 and CsGLK13 decreased in response to low-temperature induction. Taken together, the results of the transcription profile analysis suggested that CsGLK54 may play an important regulatory role under low-temperature stress. The subcellular localization of CsGLK54 was in the nucleus. Furthermore, CsGLK54 positively regulated the transcription levels of the NbPOD and NbSOD genes under low-temperature stress, which led to an increase in POD and SOD enzyme activities and a decrease in MDA content. These findings provide valuable insights into the regulatory mechanism of low-temperature stress in tea plants.

Genome-Wide Identification and Characterization of the RWP-RK Proteins in Zanthoxylum armatum.

Apomixis is a common reproductive characteristic of Zanthoxylum plants, and RWP-RKs are plant-specific transcription factors known to regulate embryonic development. However, the genome-wide analysis and function prediction of RWP-RK family genes in Z. armatum are unclear. In this study, 36 ZaRWP-RK transcription factors were identified in the genome of Z. armatum, among which 15 genes belonged to the RKD subfamily and 21 belonged to the NLP subfamily. Duplication events of ZaRWP-RK genes were mainly segmental duplication, and synteny analysis revealed a close phylogenetic relationship between Z. armatum and Arabidopsis. The analysis of cis-elements indicated that ZaRWP-RK genes may be involved in the regulation of the embryonic development of Z. armatum by responding to plant hormones such as abscisic acid, auxin, and gibberellin. Results of a real-time PCR showed that the expression levels of most ZaRWP-RK genes were significantly increased from flowers to young fruits. Protein-protein interaction network analysis further revealed the potential roles of the ZaRWP-RK proteins in apomixis. Collectively, this study is expected to improve our understanding of ZaRWP-RK transcription factors and provide a theoretical basis for future investigations into the ZaRWP-RK genes and their regulatory mechanisms in the apomixis process of Z. armatum.

Genome-wide characterisation of HD-Zip transcription factors and functional analysis of PbHB24 during stone cell formation in Chinese white pear (Pyrus bretschneideri)

BackgroundThe homodomain-leucine zipper (HD-Zip) is a conserved transcription factor family unique to plants that regulate multiple developmental processes including lignificaion. Stone cell content is a key determinant negatively affecting pear fruit quality, which causes a grainy texture of fruit flesh, because of the lignified cell walls.ResultsIn this study, a comprehensive bioinformatics analysis of HD-Zip genes in Chinese white pear (Pyrus bretschneideri) (PbHBs) was performed. Genome-wide identification of the PbHB gene family revealed 67 genes encoding PbHB proteins, which could be divided into four subgroups (I, II, III, and IV). For some members, similar intron/exon structural patterns support close evolutionary relationships within the same subgroup. The functions of each subgroup of the PbHB family were predicted through comparative analysis with the HB genes in Arabidopsis and other plants. Cis-element analysis indicated that PbHB genes might be involved in plant hormone signalling and external environmental responses, such as light, stress, and temperature. Furthermore, RNA-sequencing data and quantitative real-time PCR (RT-qPCR) verification revealed the regulatory roles of PbHB genes in pear stone cell formation. Further, co-expression network analysis revealed that the eight PbHB genes could be classified into different clusters of co-expression with lignin-related genes. Besides, the biological function of PbHB24 in promoting stone cell formation has been demonstrated by overexpression in fruitlets.ConclusionsThis study provided the comprehensive analysis of PbHBs and highlighted the importance of PbHB24 during stone cell development in pear fruits.

Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.).

The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.

Genome-Wide Identification, Expression Analysis and Functional Study of DELLA Genes in Chinese Cabbage (Brassica rapa L. ssp. pekinensis).

DELLA protein is a crucial factor which played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, little is known about the function and information of DELLA protein in Chinese cabbage. Using 5 DELLA gene sequences in Arabidopsis Thaliana as probes, 5 DELLA genes in Chinese cabbage were identified by Blast search in Chinese cabbage database (Brassica database (BRAD)). The National Center for Biotechnology Information (NCBI), ExPaSy, SWISS-MODEL, DNAMAN, MEGA 11, PlantCARE were used to identify and analyze the DELLA gene family of Chinese cabbage. Gene expression was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). The function of BraA10gRGL3 was verified by overexpression and phenotypic analysis of BraA10gRGL3 and yeast hybrid. In this study, 5 BraDELLAs homologous to Arabidopsis thaliana were identified and cloned based on the Brassica database, namely, BraA02gRGL1, BraA05gRGL2, BraA10gRGL3, BraA06gRGA and BraA09gRGA. All BraDELLAs contain the DELLA, TVHYNP, and GRAS conserved domains. Cis-element analysis revealed that the promoter regions of these 5 DELLA genes all contain light-responsive elements, TCT motif, I-box, G-box, and box 4, which are associated with GA signaling. Transcriptome analysis results proved that the expression of BraA02gRGL1, BraA05gRGL2, and BraA10gRGL3 in Y2 at different growth stages were lower than them in Y7, which is consistent with the phenotype that Y7 exhibited stronger stress tolerance than Y2. It is worth emphasizing that even through the overexpression of BraA10gRGL3-Y7 in Arabidopsis resulted in smaller leaf size and lower fresh weight compared to the wild type (WT) Arabidopsis: Columbia, a stronger response to abiotic stresses was observed in BraA10gRGL3-Y7. It indicated that BraA10gRGL3-Y7 can improve the stress resistance of plants by inhibiting their growth. Moreover, the yeast two-hybrid experiment confirmed that BraA10gRGL3-Y7 can interacted with BraA05gGID1a-Y7, BraA04gGID1b1, BraA09gGID1b3-Y2, and BraA06gGID1c, whereas BraA10gRGL3-Y2 cannot interact with any BraGID1. Collectively, BraDELLAs play important role in plant development and response to abiotic stress. The differences in amino acid sequences between BraA10gRGL3-Y2 and BraA10gRGL3-Y7 may result in variations in their protein binding sites, thus affecting their interaction with the BraGID1 family proteins. This systematic analysis lays the foundation for further study of the functional characteristics of DELLA genes of Chinese cabbage.

Genome-Wide Identification and Characterization of the PPPDE Gene Family in Rice

Protein ubiquitination is common and crucial in cellular functions, however, little is known about how deubiquitinating enzymes (DUBs) reverse regulate the ubiquitination signaling process. PPPDE family proteins are a novel class of deubiquitinating peptidases with demonstrated deubiquitination/deSUMOylating activities. In this study, we identified 10 PPPDE genes from the rice (Oryza sativa L.) genome unevenly distributed on five chromosomes, where most of these members have not been reported to date. Based on the gene structure, the OsPPPDE family consists of three distinct subgroups within the phylogenetic tree. Cis-element analysis identified light/phytohormone-responsive, development, and abiotic stress-related elements in the promoters of OsPPPDE. Furthermore, we conducted and analyzed the transcript abundance of OsPPPDE under various tissues and stresses using the transcriptome data of 352 samples from the Rice Expression Database and GEO datasets. Moreover, OsPPPDE5 showed differential regulation of its transcript abundance during Cd and drought stress. Collinearity and syntenic analysis of 101 PPPDEs and PPPDE-like proteins in 10 plant genomes indicated that this family is evolutionarily conserved. Domestication analysis suggests that OsPPPDEs may contribute to indica–japonica divergence using the data from the 3K Rice Genome Project. Our study provides a foundation for further study on the function and molecular mechanism of the OsPPPDE gene family.

GmNAC3 acts as a key regulator in soybean against drought stress

The NAC (NAM, ATAF and CUC) family is one of the largest transcription factor (TF) families in plant that are involved in the regulatory mechanisms of plant growth and development as well as responses to abiotic stresses. However, the underlying molecular mechanism of drought-responsive NAC family members in soybean still remains inexplicit. In this study, a total of 179 GmNAC genes were identified in the soybean genome. We discovered that the majority of GmNAC members have more than three exons and share a gene and motif structure that is mostly conserved at the N-terminus. Phylogenetic analysis suggested that soybean GmNAC proteins were divided into 10 separate groups. The analysis of cis-elements highlighted the potential role of GmNAC genes in various hormonal and defense related activities. In addition, most of the GmNAC genes showed notable expression in roots and leaves, suggesting their likely role in abiotic stress adaptation. The overexpression of GmNAC3-OE in Arabidopsis increased tolerance to drought stress. Similarly, the GmNAC3-OE plants displayed better survival rates, root length and antioxidant activities. Enhanced expression of stress specific genes in GmNAC3-OE was also recorded. Our findings revealed the potential role of GmNAC3 gene role in regulating soybean response to drought stress and could be used as a potential marker to generate stress resilient plants.

In silico analysis of sirtuin-type histone deacetylase genes in sugar beet (Beta vulgaris L.)

Histone deacetylase (HDAC) enzymes catalyze the removal of an acetyl group from the lysine residues of histone N-terminal tails, and they repress gene transcription through condensation of chromatin. In plants, the sirtuins/silent information regulator 2 (SIR2) proteins which are NAD+-dependent deacetylases, have been identified in distinct plant species such as Arabidopsis, rice, tomato, soybean, maize, etc., but little is known about their functions in plants. They are mainly investigated in Arabidopsis and rice and found to be involved in H3K9 acetylation, metabolic pathways, repression of genes associated with stress response, and energy metabolism. A total of eight RPD3/HDA1 family HDAC genes have been recently identified in the sugar beet (Beta vulgaris L.) genome. However, B. vulgaris SIR2-type HDACs have not yet been identified and characterized. In this work, an in silico analysis of SIR2 family members was performed in sugar beet. Three SIR2 family HDACs were identified from the sugar beet genome, named BvSRT1, BvSRT2, and BvSRT3. The beet SIR2 gene family is found to be located on chromosomes 4, and 9. The phylogenetic tree building with B. vulgaris, Arabidopsis, tomato, soybean, Vitis vinifera, pepper, rice, maize, and Sorghum bicolor showed that 3 sugar beet SRTs were divided into two classes: Class II (BvSRT2) and IV (BvSRT1 and BvSRT3). SIR2 family proteins consisted of SIR2 domain (PF02146). The conserved motifs ranged from 6 to 50 amino acids, while the intron-exon numbers of genes ranged from 10 to 14. BvSRT1 and BvSRT3 exhibited similar motif distributions and exon/intron structures. Moreover, nuclear, and cytoplasmic localization of BvSRT1 and BvSRT3 has been predicted. BvSRT2 protein was located on the mitochondrion. Analysis of cis-elements revealed the involvement of BvSRT genes in hormone regulation, light response, abiotic stress response, and meristem expression. This study may shed light on the potential role of SIR2-type HDACs in beets.

Characterization of sequences, expression profiling, and natural allelic variation analysis of the MYC gene family in sorghum (Sorghum bicolor)

Sorghum aphid (Melanaphis sacchari) and head smut fungi (Sporisorium reilianum) infesting sorghum cause delayed growth and development, and reduce yield and quality. This study use bioinformatics and molecular biological approaches to profile the gene expression pattern during sorghum development and under pest infestation, and analyzed the natural allelic DNA variation of sorghum MYC gene family. The findings provide insights for potential application in breeding the stress resistant and high productivity sorghum varieties. The results indicated that there are 28 MYC genes identified in sorghum genome, distributed on 10 chromosomes. The bHLH_MYC_N and HLH domains are the conserved domains of the MYC gene in sorghum. Gene expression analysis showed that SbbHLH35.7g exhibited high expression levels in leaves, SbAbaIn showed strong expression in early grains, and SbMYC2.1g showed high expression levels in mature pollen. In anti-aphid strains at the 5-leaf stage, SbAbaIn, SbLHW.4g and SbLHW.2g were significantly induced in leaves, while SbbHLH35.7g displayed the highest expression level in panicle tissue, which was significantly induced by the infection of head smut. Promoter cis-element analysis identified methyl jasmonate (MJ), abscisic acid (ABA), salicylic acid (SA) and MYB-binding sites related to drought-stress inducibility. Furthermore, genomic resequencing data analysis revealed natural allelic DNA variations such as single nucleotide polymorphism (SNP) and insertion-deletion (INDEL) for the key SbMYCs. Protein interaction network analysis using STRING indicated that SbAbaIn interacts with TIFYdomain protein, and SbbHLH35.7g interacts with MDR and imporin. SbMYCs exhibited temporal and spatial expression patterns and played vital roles during the sorghum development. Infestation by sugarcane aphids and head smut fungi induced the expression of SbAbaIn and SbbHLH35.7g, respectively. SbAbaIn modulated the jasmonic acid (JA) pathway to regulate the expression of defensive genes, conferring resistance to insects. On the other hand, SbbHLH35.7g participated in detoxification reactions to defend against pathogens.

Identification of Laccase Genes in Grapevine and Their Roles in Response to Botrytis cinerea

Laccases are the key enzymes responsible for plant lignin biosynthesis and responses to environment stress. However, the roles of LAC genes in plant disease resistance are still largely unknown, especially in grapevine, one of the most important horticultural crops in the world. Its quality and yield are very vulnerable to gray mold disease caused by Botrytis cinerea. In total, 30 VvLAC genes were identified and found to be unevenly distributed on seven chromosomes; they were classified into seven groups based on phylogenetic analysis according to the criteria applied in Arabidopsis thaliana. Collinearity and synteny analyses identified some orthologous gene pairs in Vitis vinifera and a few paralogous gene pairs among grape and peach. The VvLAC gene family has diverse gene structures and a highly conserved motif composition. The prominent presence of the MYB cis-elements in each VvLAC promoter highlighted MYB transcriptional factors as the main regulators of VvLAC genes. Furthermore, twenty-five VvLAC genes with functional redundancy are probably implicated in grape lignin biosynthesis. The expression patterns of the LAC genes in grape leaves of Chinese wild V. amurensis ‘Shuangyou’ (SY), a germplasm highly resistant to B. cinerea, were investigated through transcriptomic data and qRT-PCR verification. Combined with the phylogenetic analysis, with AtLACs participating in lignin metabolism, and the cis-element analysis, VaLAC14, VaLAC19, VaLAC24 and VaLAC30 were identified as key candidate genes for lignin biosynthesis in the grape response to B. cinerea. This study supplies a comprehensive understanding of the classification, evolution, structure and responses of the grape LAC genes against B. cinerea. It also provides valuable genetic resources for functional characterization towards enhancing grapevine disease resistance.

Genome-Wide Identification and Characterization of Tea SGR Family Members Reveal Their Potential Roles in Chlorophyll Degradation and Stress Tolerance

Photosynthesis plays vital roles in plant growth and development. Stay-green (SGR) proteins are responsible for chlorophyll degradation and photosynthetic metabolism. To identify SGR family members and determine their potential functions in tea plants, we identified and cloned three SGR genes. Phylogenetic analysis revealed that the tea SGR homologs were classified into the SGR subfamily (named CsSGR1 and CsSGR2) and the SGRL subfamily (named CsSGRL). Cis-element analysis indicated that the promoters of CsSGR1, CsSGR2 and CsSGRL contained light-, phytohormone- and stress-related elements. Subcellular localization confirmed that CsSGR1 was localized in the chloroplast, while CsSGR2 and CsSGRL were localized in the chloroplast, membrane and nucleus. The RT-qPCR results showed that the three genes in the matures of albino tea cultivars were expressed higher than in the green tea cultivar. However, only CsSGR2-overexpressing tobacco leaves exhibited a yellowish phenotype and significantly lower Fv/Fm values. CsSGR1 and CsSGR2 exhibited similar expression patterns in different tissues after infection with the pathogen Colletotrichum camelliae, which was opposite to the pattern observed for CsSGRL. In addition, CsSGR1 was significantly induced in response to cold stress, SA, JA and ABA in C. camelliae. These findings identified valuable candidate genes for elucidating the mechanism of leaf albinism, stress response and phytohormone signaling in tea plants.

Genome-Wide Identification and Expression Profiling of the ABF Transcription Factor Family in Wheat (Triticum aestivum L.).

Members of the abscisic acid (ABA)-responsive element (ABRE) binding factor (ABF) and ABA-responsive element binding protein (AREB) families play essential roles in the regulation of ABA signaling pathway activity and shape the ability of plants to adapt to a range of stressful environmental conditions. To date, however, systematic genome-wide analyses focused on the ABF/AREB gene family in wheat are lacking. Here, we identified 35 ABF/AREB genes in the wheat genome, designated TaABF1-TaABF35 according to their chromosomal distribution. These genes were further classified, based on their phylogenetic relationships, into three groups (A-C), with the TaABF genes in a given group exhibiting similar motifs and similar numbers of introns/exons. Cis-element analyses of the promoter regions upstream of these TaABFs revealed large numbers of ABREs, with the other predominant elements that were identified differing across these three groups. Patterns of TaABF gene expansion were primarily characterized by allopolyploidization and fragment duplication, with purifying selection having played a significant role in the evolution of this gene family. Further expression profiling indicated that the majority of the TaABF genes from groups A and B were highly expressed in various tissues and upregulated following abiotic stress exposure such as drought, low temperature, low nitrogen, etc., while some of the TaABF genes in group C were specifically expressed in grain tissues. Regulatory network analyses revealed that four of the group A TaABFs (TaABF2, TaABF7, TaABF13, and TaABF19) were centrally located in protein-protein interaction networks, with 13 of these TaABF genes being regulated by 11 known miRNAs, which play important roles in abiotic stress resistance such as drought and salt stress. The two primary upstream transcription factor types found to regulate TaABF gene expression were BBR/BPC and ERF, which have previously been reported to be important in the context of plant abiotic stress responses. Together, these results offer insight into the role that the ABF/AREB genes play in the responses of wheat to abiotic stressors, providing a robust foundation for future functional studies of these genes.

Comprehensive analysis of Brassica napus aldehyde dehydrogenase superfamily genes and demonstration of BnALDH7B2 in clubroot resistance

Oilseed rapa (Brassica napus), an important oil crop worldwide, is often threatened by various adversity stresses, especially Plasmodiophora brassicae, resulting in abnormal growth and decreased yield. The aldehyde dehydrogenase (ALDH) family is crucial for plant growth and environmental stress adaptations. Nevertheless, BnALDH members and their responses to P. brassicae are unclear in B. napus. Here, 53 B. napus ALDH members were identified and classified into 10 subfamilies. Collinearity analyses revealed that the BnALDHs gene family primarily underwent expansion through segmental duplication. Structural analyses illustrated that the BnALDHs in each specific subfamily were relatively conserved. Analysis of cis-elements in BnALDH promoter regions revealed the presence of multiple elements related to stress response and plant hormones. Transcriptome analyses indicated that BnALDHs were expressed throughout B. napus multiple tissues and growth stages. Most BnALDHs were differentially expressed under different stress treatments, with BnALDH7B2 significantly upregulated during P. brassicae stress. In addition, the BnALDH7B2 overexpression transgenic plants conferred tolerance to P. brassicae stress. Molecular docking results showed that BnALDH7B2 was more functionally dependent on NAD+ than on NADP+, while phenylacetaldehyde, benzaldehyde, trans-2-nonenal, α-aminoadipate-semialdehyde, and 4-guanidinobutyraldehyde could potentially be used as substrates for BnALDH7B2. The results provide insights into the function of BnALDHs in B. napus, serving as a baseline for identifying the functional role of BnALDH7B2 under P. brassicae stress.

Genome-Wide Identification of the DGK Gene Family in Kiwifruit (Actinidia valvata Dunn) and an Expression Analysis of Their Responses to Waterlogging Stress

Diacylglycerol kinase (DGK) is a lipid kinase that phosphorylates diacylglycerol (DAG) to generate phosphatidic acid (PA). Based on converting one important signaling molecule (DAG) to another (PA), DGK plays an important role in plant responses to abiotic stress, including waterlogging stress. However, no studies have been reported on the characterization of the DGK gene family in the waterlogging-tolerant kiwifruit germplasm Actinidia valvata Dunn. In this study, we identified 18 AvDGK genes in the A. valvata genome. The phylogenetic analysis showed that AvDGKs can be classified into three clusters, and members within the same cluster have similar domain distributions, exon-intron structures, and conserved motif compositions. The chromosome localization analysis revealed that all AvDGK genes are located across 18 different chromosomes. There were 29 duplicated gene pairs in A. valvata and all had undergone purifying selection during evolution. The promoter cis-element analysis revealed that the cis-elements within AvDGK genes are associated with multiple functions, including phytohormone signal transduction, stress responses, and plant growth and development. The expression pattern analyses indicated that AvDGKs play important roles in fruit development and plant responses to waterlogging stress. The AvDGK gene family in the tetraploid A. valvata genome might promote PA synthesis and subsequent signal transduction both under short- and long-term waterlogging stresses. These results provide information regarding the structural characteristics and potential function of AvDGK genes within A. valvata and lay a fundamental basis for further research into breeding to enhance the kiwifruit’s tolerance to waterlogging stress.

Identification of the ERF gene family of Mangifera indica and the defense response of MiERF4 to Xanthomonas campestris pv. mangiferaeindicae

An important regulatory role for ethylene-responsive transcription factors (ERFs) is in plant growth and development, stress response, and hormone signaling. However, AP2/ERF family genes in mango have not been systematically studied. In this study, a total of 113 AP2/ERF family genes were identified from the mango genome and phylogenetically classified into five subfamilies: AP2 (28 genes), DREB (42 genes), ERF (33 genes), RAV (6 genes), and Soloist (4 genes). Of these, the ERF family, in conjunction with Arabidopsis and rice, forms a phylogenetic tree divided into seven groups, five of which have MiERF members. Analysis of gene structure and cis-elements showed that each MiERF gene contains only one AP2 structural domain, and that MiERF genes contain a large number of cis-elements associated with hormone signaling and stress response. Collinearity tests revealed a high degree of homology between MiERFs and CsERFs. Tissue-specific and stress-responsive expression profiling revealed that MiERF genes are primarily involved in the regulation of reproductive growth and are differentially and positively expressed in response to external hormones and pathogenic bacteria. Physiological results from a gain-of-function analysis of MiERF4 transiently overexpressed in tobacco and mango showed that transient expression of MiERF4 resulted in decreased colony count and callose deposition, as well as varying degrees of response to hormonal signals such as ETH, JA, and SA. Thus, MiERF4 may be involved in the JA/ETH signaling pathway to enhance plant defense against pathogenic bacteria. This study provides a basis for further research on the function and regulation of MiERF genes and lays a foundation for the selection of disease-resistant genes in mango.

Genome-wide analysis of the C2H2-ZFP gene family in Stevia rebaudiana reveals involvement in abiotic stress response

Stevia (Stevia rebaudiana Bertoni) is a natural sweetener plant that accumulates highly sweet steviol glycosides (SGs) especially in leaves. Stevia is native to humid areas and does not have a high tolerance to drought which is the most serious abiotic stress restricting its production worldwide. C2H2 zinc finger proteins (C2H2-ZFPs) are a group of well-known transcription factors that involves in various developmental, physiological and biochemical activities as well as in response to abiotic stresses. Here we analyzed C2H2-ZFP gene family in stevia and identified a total of 185 putative SrC2H2-ZF proteins from the genome sequence of S. rebaudiana. We further characterized the identified C2H2-ZF domains and their organization, additional domains and motifs and analyzed their physicochemical properties, localization and gene expression patterns. The cis-element analysis suggested multiple roles of SrC2H2-ZFPs in response to light, phytohormone, and abiotic stresses. In silico analysis revealed that the stevia C2H2-ZFP genes are interactively expressed in different tissues and developmental stages and some C2H2-ZFP genes are involved in response to drought stress. This study provides a background for future exploration of the functional, and regulatory aspects of the C2H2-ZFP gene family in S. rebaudiana.

Identification and Characterization of the AREB/ABF Gene Family in Three Orchid Species and Functional Analysis of DcaABI5 in Arabidopsis.

AREB/ABF (ABA response element binding) proteins in plants are essential for stress responses, while our understanding of AREB/ABFs from orchid species, important traditional medicinal and ornamental plants, is limited. Here, twelve AREB/ABF genes were identified within three orchids' complete genomes and classified into three groups through phylogenetic analysis, which was further supported with a combined analysis of their conserved motifs and gene structures. The cis-element analysis revealed that hormone response elements as well as light and stress response elements were widely rich in the AREB/ABFs. A prediction analysis of the orchid ABRE/ABF-mediated regulatory network was further constructed through cis-regulatory element (CRE) analysis of their promoter regions. And it revealed that several dominant transcriptional factor (TF) gene families were abundant as potential regulators of these orchid AREB/ABFs. Expression profile analysis using public transcriptomic data suggested that most AREB/ABF genes have distinct tissue-specific expression patterns in orchid plants. Additionally, DcaABI5 as a homolog of ABA INSENSITIVE 5 (ABI5) from Arabidopsis was selected for further analysis. The results showed that transgenic Arabidopsis overexpressing DcaABI5 could rescue the ABA-insensitive phenotype in the mutant abi5. Collectively, these findings will provide valuable information on AREB/ABF genes in orchids.

Deciphering the regulatory role of PheSnRK genes in Moso bamboo: insights into hormonal, energy, and stress responses

The SnRK (sucrose non-fermentation-related protein kinase) plays an important role in regulating various signals in plants. However, as an important bamboo shoot and wood species, the response mechanism of PheSnRK in Phyllostachys edulis to hormones, low energy and stress remains unclear. In this paper, we focused on the structure, expression, and response of SnRK to hormones and sugars. In this study, we identified 75 PheSnRK genes from the Moso bamboo genome, which can be divided into three groups according to the evolutionary relationship. Cis-element analysis has shown that the PheSnRK gene can respond to various hormones, light, and stress. The PheSnRK2.9 proteins were localized in the nucleus and cytoplasm. Transgenic experiments showed that overexpression of PheSnRK2.9 inhibited root development, the plants were salt-tolerant and exhibited slowed starch consumption in Arabidopsis in the dark. The results of yeast one-hybrid and dual luciferase assay showed that PheIAAs and PheNACs can regulate PheSnRK2.9 gene expression by binding to the promoter of PheSnRK2.9. This study provided a comprehensive understanding of PheSnRK genes of Moso bamboo, which provides valuable information for further research on energy regulation mechanism and stress response during the growth and development of Moso bamboo.

Genome-Wide Identification and Drought Stress Response Pattern of the NF-Y Gene Family in Cymbidium sinense.

Cymbidium sinense, a type of orchid plant, is more drought-resistant and ornamental than other terrestrial orchids. Research has shown that many members of the NUCLEAR FACTOR Y (NF-Y) transcription factor family are responsive to plant growth, development, and abiotic stress. However, the mechanism of the NF-Y gene family's response to abiotic stress in orchids has not yet been reported. In this study, phylogenetic analysis allowed for 27 CsNF-Y genes to be identified (5 CsNF-YAs, 9 CsNF-YBs, and 13 CsNF-YC subunits), and the CsNF-Ys were homologous to those in Arabidopsis and Oryza. Protein structure analysis revealed that different subfamilies contained different motifs, but all of them contained Motif 2. Secondary and tertiary protein structure analysis indicated that the CsNF-YB and CsNF-YC subfamilies had a high content of alpha helix structures. Cis-element analysis showed that elements related to drought stress were mainly concentrated in the CsNF-YB and CsNF-YC subfamilies, with CsNF-YB3 and CsNF-YC12 having the highest content. The results of a transcriptome analysis showed that there was a trend of downregulation of almost all CsNF-Ys in leaves under drought stress, while in roots, most members of the CsNF-YB subfamily showed a trend of upregulation. Additionally, seven genes were selected for real-time reverse transcription quantitative PCR (qRT-PCR) experiments. The results were generally consistent with those of the transcriptome analysis. The regulatory roles of CsNF-YB 1, 2, and 4 were particularly evident in the roots. The findings of our study may make a great contribution to the understanding of the role of CsNF-Ys in stress-related metabolic processes.