Cis-element Analysis Research Articles

Comparative analysis of IRE1s in plants: insights into heat stress adaptation in Triticum aestivum.

The unfolded protein response (UPR) pathway serves as a crucial mechanism enabling plants to perceive, respond to, and shield themselves from adverse environmental conditions. Inositol-requiring enzyme 1 (IRE1) is one of the key players of the UPR, and resides in the endoplasmic reticulum (ER) within the cell. This study provides a comprehensive analysis of 195 IRE1 genes across 90 diverse plant species, with a focus on their identification and characterization. To decipher the functions of IRE1 family members, we investigated the evolution and spread of IREs in plants and analysed their structural and localization characteristics. Our detailed cis-element analysis revealed unique IRE1 regulation patterns in different plant species. Furthermore, gene expression analysis revealed tissue-specific and heat stress-responsive expression patterns of TaIRE1s, which were subsequently confirmed via quantitative gene expression analysis. TaIRE1-6A was upregulated in response to dithiothreitol (DTT) treatment as well as heat stress. This finding suggests that IRE1 might play a role in linking the UPR pathway and the heat stress response (HSR). Our findings provide a comprehensive understanding of the evolution and expansion of IRE1 genes in different plant species. These findings provide a foundation for further in-depth research on the functional diversity of IREs in nutritious crops following polyploidization. By linking the UPR with HSR, IRE1 could be a key contributor to wheat's resilience against heat stress. Additionally, this connection offers important insights for future functional studies in other crops. Thus, this knowledge could be used for engineering climate resilience in crops such as wheat.

PP2 gene family in Phyllostachys edulis: identification, characterization, and expression profiles.

Phloem protein 2 (PP2), a dimeric lectin, is known for its involvement in plant responses to biotic and abiotic stresses. However, research on PP2 proteins in Moso bamboo is lacking. In this study, comprehensive genome-wide analysis of the PP2-like gene family was conducted in Moso bamboo (Phyllostachys edulis), which has a significant economic and ecological value. Using HMMER3 search and InterPro domain analysis, 23 PP2-like genes (PhePP2-1 to PhePP2-23) were identified in the P. edulis genome. These genes were distributed across 12 chromosomal scaffolds, with proteins ranging from 216 to 556 amino acids in length. Phylogenetic analysis, including 163 PP2 proteins from eight plant species, revealed six distinct groups, with Group III and Group V being the largest. Gene structure and motif analyses indicated conserved domains across the PhePP2 proteins. In addition, Cis-element analysis of the promoter regions highlighted their potential regulatory roles in hormone, stress, and light responses. Expression pattern analysis using RNA-seq data showed differential expression of PhePP2 genes under drought, salt, salicylic acid, and abscisic acid treatments, indicating their involvement in stress response pathways. Furthermore, qPCR validation in different tissues and organs of Moso bamboo confirmed the expression profiles of the selected PhePP2 genes. This study provides a comprehensive understanding of the functional roles of PP2-like genes in Moso bamboo and insights into their potential applications in enhancing stress tolerance and growth in plants.

Transcriptome and genome-wide analysis of the mango glycosyltransferase family involved in mangiferin biosynthesis.

Mangiferin, a C-glucosyl xanthone, is a biologically active glycoside naturally synthesized in mango. Glycosyltransferase can catalyze the biosynthesis of mangiferin. In this study, we identified 221 members of the UGT glycosyltransferase family in mango. The 221 MiUGT genes were grouped into 13 subfamilies through phylogenetic tree analysis with Arabidopsis, Chinese bayberry, and mango. All UGT family members in mango were unevenly distributed on 17 chromosomes and found that tandem duplication dominated the expansion of UGT family members in mango. Purification selection primarily influenced the evolution of the mango UGT family members. In addition, cis-element analysis of the mango UGT gene family revealed the presence of MYB binding sites, which are involved in flavonoid biosynthesis; which further supports the role of UGT family members in the synthesis of flavonoids. To verify these results, we analyzed the expression of UGT family members in mango leaves, stems, and different developmental stages of fruit peel. The RNA-seq and qRT-PCR results showed significant differences in the expression patterns of MiUGT genes in various tissues and developmental stages of mango. We identified MiUGT gene-specific expression at different stages of fruit development. These results lay a theoretical foundation for research on the relationship between members of the mango UGT family and the synthesis of flavonoids, mangiferin.

Genome-wide comparative analysis of photosynthetic enzymatic genes provides novel insights into foxtail millet and other cereals

C4 crops have more efficient photosynthetic pathways that enable their higher photosynthetic capacities as well as nitrogen and water use efficiencies than C3 crops. Previous research has demonstrated that the genomes of C3 species include and express every gene needed for the C4 photosynthesis pathway. However, very little is known about the dynamics and evolutionary history of such genetic evolution in C4 plants. In this study, the genes encoding five key photosynthetic pathway enzymes in the genomes of C3 (rice), C4 (maize, sorghum, and foxtail millet), and CAM (pineapple) crops were identified and compared systematically. The numbers of genes in these photosynthetic enzymes were highest in the C4 crops like sorghum and foxtail millet, while only eight genes were identified in the CAM plant. However, 16 genes were identified in the C3 crop rice. Furthermore, we performed physical, chemical, gene structure and, cis-element analyses to obtain complete insights into these key genes. Tissue-specific expressions showed that most of the photosynthetic genes are expressed in the leaf tissues. Comparisons of the expression characteristics confirmed that the expression patterns of non-photosynthetic gene copies were relatively conserved among the species, while the C4 gene copies in the C4 species acquired new tissue expression patterns during evolution. Additionally, multiple sequence features that could affect C4 gene expressions and subcellular localization were found in the coding and promoter regions. Our research also highlights the variations in how different genes have evolved within the C4 photosynthetic pathway, and we confirmed that specific high expressions in the leaves and right distribution within the cells were crucial for the development of the C4 photosynthetic abilities. The findings of this study are expected to aid in understanding the evolutionary process of the C4 photosynthetic pathway in grasses as well as offer insights for modifying the C4 photosynthetic pathways in wheat, rice, and other significant C3 cereal crops.

Unveiling the camelina MBOAT gene family: Phylogenetic insights and regulatory landscape

The membrane-bound O-acyltransferase (MBOAT) gene family comprises enzymes responsible for transferring acyl groups to various lipid molecules. Some members of the MBOAT gene family and their functions have been extensively studied in the model plant Arabidopsis. However, research on the MBOAT gene family in camelina is still limited. In this study, 54 MBOATs were identified on 17 chromosomes and one unidentified scaffold in camelina, including seven newly identified genes. A total of 149 MBOATs were identified in 10 other species. Six subgroups of these MBOATs with different conservation were classified by phylogenetic analysis, showing diversification between monocots and dicots. Detailed analysis of the motif composition, evolutionary relationships, and gene structures of CsaMBOATs are presented. The results of the syntenic analysis suggest that the evolution of CsaMBOAT gene family is primarily driven by segmental and tandem duplications, and that there is a stronger collinearity within dicots. In addition, analysis of CsaMBOAT gene promoter cis-elements reveals a possible transcriptional regulation and tissue-specific expression, highlighting potential role in plant stress responses and hormone signaling. Furthermore, both the transcriptome and RT-qPCR data revealed the changes in the expression levels of DGAT1 during salt stress treatment. Subsequent analyses indicated that DGAT1 influenced the ratio of fatty acid fractions in the plants. Importantly, a large number of transcription factors involved in the regulation of CsaMBOAT gene expression were identified by WGCNA analysis, and the transcriptional data confirmed that the NAC032 and CAMMTA6 genes play a role upstream of DGAT1. This study not only identified the members of the MBOAT in camelina, but also provided insights and clues into its regulatory mechanisms.

Comprehensive analysis of Capsicum annuum CaLhcs uncovered the roles of CaLhca5.1 and CaLhcb1.7 in photosynthesis and stress tolerance

The light-harvesting chlorophyll a/b-binding proteins (Lhcs) are integral to plants' capture and transfer of light energy during photosynthesis. However, the Lhc gene family remains unexplored in pepper. In this study, 37 CaLhcs (Capsicum annuum Lhc) were identified from the reference genome and classified into five subfamilies (Lhca, Lhcb, CP24, CP26, and CP29) based on phylogenetic relationships and conserved domains, with members of each subfamily displaying similar conserved motifs and gene structures. cis-element analysis revealed an enrichment of light-responsive elements within CaLhcs (46.1 %). Transcriptome analysis showed that most CaLhcs are specifically expressed in leaves, flowers, and pericarp and are responsive to stressors, including NaCl, cold, heat, H2O2, and d-mannitol. Post-transcriptional regulation analysis identified 11 miRNAs that target nine CaLhcs through cleavage. RT-qPCR analysis validated the involvement of CaLhcs in response to NaCl stress. Localization studies confirmed that CaLhca4.1, CaLhcb1.1, CaLhca1.7, CaLhcb1.11, and CaLhcb6.1 are chloroplast-localized, whereas CaLhca5.1 localizes in the nucleus. Overexpression of CaLhcb1.7 and CaLhca5.1 increased chlorophyll content and net photosynthetic rate, enhancing photosynthesis. Additionally, CaLhcb1.7 and CaLhca5.1 reduced ROS accumulation, bolstering the plant's resistance to pathogens and salt stress. These findings provide a foundation for further exploration of CaLhcs in photosynthesis and stress tolerance mechanisms.

Epigenomic studies in sorghum reveal differential enrichment of multiple histone marks at clade A PP2C genes in response to drought

Epigenetic regulation is essential for plant development and stress responses, as numerous stress-responsive genes are modulated epigenetically. However, most research has focused on individual histone marks. This study expands on previous work by examining the genome-wide profiles of seven histone marks (H3K9ac, H3K27ac, H3K4me3, H3K36me3, H3K27me3, H2A.Z, and H3K4me2) in sorghum leaves and roots under PEG-induced drought stress. Results revealed that five histone marks (excluding H3K36me3 and H3K27me3) were significantly associated with drought-responsive gene expression. The differential enrichment of these marks may enhance the induction of drought-responsive genes. Specifically, a subset of genes showed multiple histone marks' differential enrichment, with most clade A PP2C genes exhibiting enrichment for four marks after PEG treatment. This suggests a critical role for robust PP2C gene induction in sorghum’s drought response. Additionally, promoter cis-element analysis identified ERF family transcription factors as potential mediators of histone mark enrichment under drought conditions, providing new insights into the interaction between epigenetic modifications and transcriptional regulation in plant stress responses.

Genome-Wide Characterization of Shi-Related Sequence Gene Family and Its Roles in Response to Zn2+ Stress in Cucumber

Shi-related sequence (SRS) proteins, which consist of the RING-like zinc finger domain and IGGH domain, are plant-specific transcription factors that have been well-studied in several plant species. However, information about SRS genes and their roles in cucumber (Cucumis sativus L.) is limited. Therefore, we performed detailed bioinformatic analysis of the SRS gene family, including gene numbers and positions, genes structures, conserved motif distribution patterns, phylogenetic analysis, and promoter cis-element analysis. Eight SRS genes were identified in cucumber and distributed on all seven cucumber chromosomes. SRS genes are conserved in plants and divided into two groups in cucumber based on their protein sequence. In silico analysis predicted that most genes may function in response to abiotic stresses and phytohormones. Gene ontology analysis predicted the possible involvement of genes in development and reproduction, and DNA and protein binding on a molecular level. Furthermore, the differential expression pattern of SRS genes in leaf, stem and root under the condition of Zn2+ stress suggested their roles in response to Zn2+ stress. Furthermore, our metal tolerance assay suggested that CsSRS2 and CsSRS5 mediated enhanced tolerance to Zn2+ stress in Escherichia coli cells. Our study provides a foundation for the functional study of SRS genes in cucumber.

Characterization of Cytoskeletal Profilin Genes in Plasticity Elongation of Mesocotyl and Coleoptile of Maize Under Diverse Abiotic Stresses.

The plasticity elongation of mesocotyl (MES) and coleoptile (COL) largely determines the morphology of maize seedlings under abiotic stresses. The profilin (PRF) proteins play a pivotal role in cytoskeleton dynamics and plant development via regulating actin polymerization. However, little is known about whether and how the expression of the ZmPRF gene family regulates MES and COL elongation in maize under adverse abiotic stresses. Here, a total of eight ZmPRF gene members were identified in the maize genome. They were mainly located in the cytoplasm, chloroplast, and mitochondrion, and clearly divided into four classes, based on phylogenetic analysis. Segmental duplication was the main driver for the expansion of ZmPRF genes. Ka/Ks analysis indicated that most ZmPRF genes were intensely purified and selected. Promoter cis-element analysis suggested their potential roles in response to growth and development, stress adaption, hormone response, and light response. The protein-protein interaction network and two independent RNA-sequencing analyses revealed that eight ZmPRF genes and their thirty-seven interacting genes showed varied expression patterns in MES and COL of three maize genotypes under different sowing depths, 24-epibrassinolide application, and light spectral-quality treatments, of which ZmPRF3.3 was a potential core conserved gene for breeding application. Moreover, the quantitative real-time PCR (qRT-PCR) verified that the relative expression levels of most ZmPRF genes in MES and COL under above treatments were significantly correlated with the plasticity elongation of MES and COL in maize. Therefore, these results perform a comprehensive overview of the ZmPRF family and will provide valuable information for the validation of the function of ZmPRF genes in maize development under diverse abiotic stress.

Evolutionary and Expression Analyses of the bZIP Family in Tea Plants (Camellia sinensis) and Functional Characterization of CsbZIP3/42/6 in Response to Environmental Stresses.

Basic leucine zipper (bZIP) transcription factors play crucial roles in various biological processes and responses to environmental stresses. However, the functions of the bZIP family in tea plants remain largely unexplored. Here, we identified 74 bZIP genes in tea plants (Camellia sinensis) and classified them into 12 phylogenetic groups, supported by analyses of conserved motifs and gene structures. Cis-element analysis provided insights into the potential roles of CsbZIP genes in phytohormone signaling and stress responses. Tissue-specific expression analysis demonstrated differential expression profiles of CsbZIP genes, suggesting their tissue- and stage-specific functions. Additionally, varying expression levels under different abiotic stresses indicated functional divergence of the CsbZIP family during the long-term evolution. Notably, CsbZIP3/42/6 were identified as positive regulators of drought and salt stress responses but negative regulators in response to pathogen infection, and CsbZIP42 could interact with CsbZIP3 and CsbZIP6 in regulating these environmental stresses. This study provides valuable information on potential applications for improving stress tolerance and overall plant health of tea plants.

Genome-wide exploration of the CONSTANS-like (COL) gene family and its potential role in regulating plant flowering time in foxtail millet (Setaria italica)

In photoperiod-sensitive plants, the CO-like gene (CONSTANS-like, COL) has a crucial function in regulating the timing of flowering. The blooming period in foxtail millet is greatly influenced by the duration of daylight; however, there is a scarcity of data regarding the molecular properties of the COL genes in the foxtail millet. In this study, we conducted a comprehensive analysis of the COL gene family in foxtail millet at the genome-wide level. We identified 11 SiCOL genes and performed gene structure analysis, which showed pronounced variation in gene length and intron number among the genes. The examination of COL proteins in foxtail millet and other plant species using phylogenetic analysis revealed that they could be clustered into three distinct groups. Cis-element analysis identified elements related to light-responsiveness, hormones, and abiotic stress in the promoter region of the SiCOL gene. Furthermore, tissue-specific expression analysis showed widespread expression of all 11 SiCOL genes in various foxtail millet tissues and organs, particularly in leaves and panicles. Collinearity analysis identified 14 syntenic gene pairs in both foxtail millet and rice. The results also revealed diurnal oscillations in the transcription levels of SiCOL genes under different light conditions. Moreover, among the 11 genes, SiCO, SiCOL1, and SiCOL6 expression levels were negatively correlated with flowering time variation in two foxtail cultivars. Additionally, upon constructing a network of predicted molecular interactions, FLOWER LOCUS-like (FTL) and Phytochromea A (PHY A) were suggested to potentially interact with SiCO, SiCOL1, and SiCOL6. SiCO, SiCOL1, and SiCOL6 have the potential for flowering and heading in foxtail millet. This research enhances our comprehension of the role and control of the SiCOL gene family constituents in foxtail millet, establishing a basis for future investigations.

Genome-Wide Identification of the Peanut ASR Gene Family and Its Expression Analysis under Abiotic Stress.

Peanut (Arachis hypogaea L.) is one of the most important oil and food legume crops worldwide. ASR (abscisic acid, stress, ripening) plays extremely important roles in plant growth and development, fruit ripening, pollen development, and stress. Here, six ASR genes were identified in peanut. Structural and conserved motif analyses were performed to identify common ABA/WDS structural domains. The vast majority of ASR genes encoded acidic proteins, all of which are hydrophilic proteins and localized on mitochondria and nucleus, respectively. The cis-element analysis revealed that some cis-regulatory elements were related to peanut growth and development, hormone, and stress response. Under normal growth conditions, AhASR4 and AhASR5 were expressed in all tissues of peanut plants. Quantitative real-time PCR (qRT-PCR) results indicated that peanut ASR genes exhibited complex expression patterns in response to abiotic stress. Notably, under drought and cadmium (Cd) stress, the expression levels of AhASR4 and AhASR5 were significantly upregulated, suggesting that these genes may play a crucial role in the peanut plant's resistance to such stressors. These results provide a theoretical basis for studying the evolution, expression, and function of the peanut ASR gene family and will provide valuable information in the identification and screening of genes for peanut stress tolerance breeding.

Comprehensive analysis of ankyrin repeat gene family revealed SbANK56 confers drought tolerance in sorghum

Ankyrin repeat (ANK) proteins are crucial for cell growth, development, and response to hormones and environmental stress. However, there has been little research done to clarify the roles of ANK proteins in sorghum. In this study, 142 ANK genes of sorghum were identified and classified into 12 subfamilies according to the conserved domains. The cis-elements analysis revealed a substantial presence of stress-responsive elements within the promoter region of SbANK genes. After treated with drought, salt, and abscisic acid, SbANK56 showed the highest expression levels among family members by using quantitative real-time PCR (qRT-PCR) analysis. The survival rate was significantly improved by the overexpression of SbANK56 compared to wild type (WT) under drought conditions. SbANK56 overexpressing plants displayed lower malondialdehyde and higher proline contents compared to WT plants under drought conditions. Additionally, the expression levels of drought-associated genes were significantly increased in SbANK56 transgenic plants. Importantly, the analysis of natural variation in SbANK56 revealed a significant positive correlation between SbANK56Hap4 and both its differential expression and drought stress tolerance. Taken together, our results provide some evidence for improving drought tolerance in sorghum through breeding initiatives while also advancing our knowledge of the evolutionary trends and functional mechanisms underlying ANK genes.

Genome-wide analysis of the MADS-box gene family in mango and ectopic expression of MiMADS77 in Arabidopsis results in early flowering

Mango (Mangifera indica L.) is an important tropical fruit, and timely flowering and fruit setting are very important for mango production. The MADS-box gene family is involved in the regulation of flower induction, floral organ specification, and fruit development in plants. The identification and analysis of the MADS-box gene family can lay a foundation for the study of the molecular mechanism of flowering and fruit development in mango. In this study, 119 MiMADS-box genes were identified on the basis of genome and transcriptome data. Phylogenetic analysis revealed that these genes can be divided into two classes. Forty-one type I proteins were further divided into three subfamilies, and seventy-eight type II proteins were further classified into eleven subfamilies. Several pairs of alternative splicing genes were found, especially in the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) subfamily. The MiMADS-box genes were distributed on 18 out of the 20 mango chromosomes. Cis-element analysis revealed many light-, stress-, and hormone-responsive elements in the promoter regions of the mango MiMADS-box genes. Expression pattern analysis revealed that these genes were differentially expressed in multiple tissues in mango. The highly expressed MiMADS77 was subsequently transformed into Arabidopsis, resulting in significant early flowering and abnormal floral organs. Yeast two-hybrid (Y2H) assays revealed that MiMADS77 interacts with several MiMADS-box proteins. In addition, we constructed a preliminary flowering regulatory network of MADS-box genes in mango on the basis of related studies. These results suggest that MiMADS77 genes may be involved in flowering regulation of mango.

Bioinformatics Analysis and Expression Features of Terpene Synthase Family in Cymbidium ensifolium

Terpene synthases (TPSs) are crucial for the diversification of terpenes, catalyzing the formation of a wide variety of terpenoid compounds. However, genome-wide systematic characterization of TPS genes in Cymbidium ensifolium has not been reported. Within the genomic database of C. ensifolium, we found 30 CeTPS genes for this investigation. CeTPS genes were irregularly distributed throughout the seven chromosomes and primarily expanded through tandem duplications. The CeTPS proteins were classified into three TPS subfamilies, including 17 TPS-b members, 8 TPS-a members, and 5 TPS-c members. Conserved motif analysis showed that most CeTPSs contained DDxxD and RRX8W motifs. Cis-element analysis of CeTPS gene promoters indicated regulation primarily by plant hormones and stress. Transcriptome analysis revealed that CeTPS1 and CeTPS18 had high expression in C. ensifolium flowers. qRT-PCR results showed that CeTPS1 and CeTPS18 were predominantly expressed during the flowering stage. Furthermore, CeTPS1 and CeTPS18 proteins were localized in the chloroplasts. These results lay the theoretical groundwork for future research on the functions of CeTPSs in terpenoid biosynthesis.

Genome‑wide analysis of cotton SCAMP genes and functional characterization of GhSCAMP2 and GhSCAMP4 in salt tolerance

BackgroundSecretory carrier membrane proteins (SCAMPs) form a family of integral membrane proteins and play a crucial role in mediating exocytosis in both animals and plants. While SCAMP genes have been studied in several plant species, their functions in cotton, particularly in response to abiotic stress, have not yet been reported.ResultsIn this study, a total of 53 SCAMP genes were identified in G. arboreum, G. raimondii, G. hirsutum, and G. barbadense. These genes were classified into five groups based on a phylogenetic analysis with SCAMPs from Arabidopsis thaliana. The main factor driving the expansion of the SCAMP gene family in G. hirsutum is tandem and segmental duplication events. Using MEME, in addition to the conserved SCAMP domain, we identified 3–13 other domains in each GhSCAMP. The cis-element analysis suggested that GhSCAMPs were widely involved in cotton growth and development, and responses to abiotic stresses. RNA sequencing (RNA-Seq) and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) results showed that most GhSCAMPs were expressed highly in many tissues and had differential expression responses to drought, cold, and heat stresses. Knock-down of GhSCAMP2 and GhSCAMP4 by virus-induced gene silencing (VIGS) lead to a salt-sensitive phenotype and had a lower content of CAT, POD, and SOD.ConclusionsThis study identified SCAMP genes in four cotton species, enhancing our understanding of the potential biological functions of SCAMPs. Additionally, we demonstrated that GhSCAMP2 and GhSCAMP4 positively regulate cotton tolerance to salt stress.

Genome-wide identification and characterization of pectin methylesterase inhibitor gene family members related to abiotic stresses in watermelon.

Pectin is a vital component of plant cell walls and its methylation process is regulated by pectin methylesterase inhibitors (PMEIs). PMEIs regulate the structural and functional modifications of cell walls in plants and play an important role in plant processes such as seed germination, fruit ripening, and stress response. Although the PMEI gene family has been well characterized in model plants, the understanding of its molecular evolution and biological functions in watermelon remains limited. In this study, 60 ClPMEI genes were identified and characterized, revealing their dispersion on multiple chromosomes. Based on a systematic developmental analysis, these genes were classified into three subfamilies, which was further supported by the exon, intron, and conserved motif distribution. Analysis of cis-elements and expression patterns indicated that ClPMEIs might be involved in regulating the tolerance of watermelon to various abiotic stresses. Moreover, distinct ClPMEI genes exhibit specific functions under different abiotic stresses. For example, ClPMEI51 and ClPMEI54 showed a significant upregulation in expression levels during the late stage of drought treatments, whereas ClPMEI3 and ClPMEI12 displayed a significant downregulation under low-temperature induction. Subcellular localization prediction and analysis revealed that the ClPMEI family member proteins were localized to the cell membrane. This study provided an important foundation for the further exploration of the functions of ClPMEI genes in watermelon.

Comparative Analysis of Casparian Strip Membrane Domain Protein Family in Oryza sativa (L.) and Arabidopsis thaliana (L.).

The Casparian strip membrane domain proteins (CASPs) are pivotal for the formation of the Casparian strip (CS) in endodermal cells and play a crucial role in a plant's response to environmental stresses. However, existing research on the CASP gene family in rice and Arabidopsis lacks a comprehensive bioinformatics analysis and necessitates further exploration. In this study, we identified 41 OsCASP and 39 AtCASP genes, which were grouped into six distinct subgroups. Collinearity analysis underscored the pivotal roles of WGD and TD events in driving the evolution of CASPs, with WGDs being the dominant force. On the one hand, the analysis of cis-elements indicated that most OsCASP and AtCASP genes contain MYB binding motifs. On the other hand, RNA-seq revealed that the majority of OsCASP and AtCASP genes are highly expressed in roots, particularly in endodermal cells, where OsCASP_like11/9 and AtCASP_like1/31 demonstrated the most pronounced expression. These results suggest that OsCASP_like11/9 and AtCASP_like1/31 might be candidate genes involved in the formation of the endodermis CS. RT-qPCR results demonstrated that OsCASP_like2/3/13/17/21/30 may be candidate genes for the ion defect process. Collectively, this study offers a theoretical foundation for unraveling the biological functions of CASP genes in rice and Arabidopsis.

Genome-Wide Identification of the Soybean AlkB Homologue Gene Family and Functional Characterization of GmALKBH10Bs as RNA m6A Demethylases and Expression Patterns under Abiotic Stress.

Soybean (Glycine max (L.) Merr) is one of the most important crops worldwide, but its yield is vulnerable to abiotic stresses. In Arabidopsis, the AlkB homologue (ALKBH) family genes plays a crucial role in plant development and stress response. However, the identification and functions of its homologous genes in soybean remain obscured. Here, we identified a total of 22 ALKBH genes in soybean and classified them into seven subfamilies according to phylogenetic analysis. Gene duplication events among the family members and gene structure, conserved domains, and motifs of all candidate genes were analyzed. By comparing the changes in the m6A levels on mRNA from hair roots between soybean seedlings harboring the empty vector and those harboring the GmALKBH10B protein, we demonstrated that all four GmALKBH10B proteins are bona fide m6A RNA demethylases in vivo. Subcellular localization and expression patterns of the GmALKBH10B revealed that they might be functionally redundant. Furthermore, an analysis of cis-elements coupled with gene expression data demonstrated that GmALKBH10B subfamily genes, including GmALKBH10B1, GmALKBH10B2, GmALKBH10B3, and GmALKBH10B4, are likely involved in the cis-elements' response to various environmental stimuli. In summary, our study is the first to report the genome-wide identification of GmALKBH family genes in soybean and to determine the function of GmALKBH10B proteins as m6A RNA demethylases, providing insights into GmALKBH10B genes in response to abiotic stresses.

Whole-genome characterization of CKX genes in Prunus persica and their role in bud dormancy and regrowth

Dud dormancy is a complex physiological process of perennial woody plants living in temperate regions, and can be affected by various phytohormones. Cytokinin oxidase/dehydrogenases (CKXs) are a group of enzymes essential for maintaining cytokinin homeostasis, but a comprehensive analysis in peach is lacking. Here, a total of 51 CKX members from different species, including six from peach, eleven from apple, nine from poplar, seven from Arabidopsis, eight from strawberry and ten from rice, which were identified using The Simple HMM Search tool of TBtools and a BLASTP program, were classified into four groups using phylogenetic analysis. Conserved motif and gene structure analysis of these 51 CKX members showed that ten conserved motifs were identified, and each CKX gene contained at least two introns. Cis-element analysis of PpCKXs showed that all of the PpCKX genes have light-responsive elements and at least one hormone-responsive element. The obviously changed relative expression <pg=>levels of six PpCKX genes in peach buds from endodormancy to bud-break were observed by qRT-PCR. Among them, the expression trend of PpCKX6 was almost opposite that of PpEBB1, a positive bud-break regulator in woody plants, around the bud-break stage. Y1H, EMSA, and dual-luciferase assays indicated that PpEBB1 negatively regulated PpCKX6 through direct binding to a GCC box-like element located in the promoter region of PpCKX6. In addition, a transient assay showed that overexpression of PpCKX6 delayed bud-break of peach. These results indicate that the PpCKX genes play an important role in the dormancy-regrowth process and PpCKX6 may act downstream of PpEBB1 directly to regulate bud-break process, which further improves the hormone-regulatory network of dormancy-regrowth of woody plants, and provides new insights for molecular breeding and genetic engineering of peach.