Search Results (37)

The SHORT INTERNODES-related sequence (SRS) gene family, comprising zinc finger and IXGH domain-containing transcription factors, serves as a critical regulator of plant biological processes and abiotic stress responses. In this study, the common wheat cultivar Chinese Spring was selected as the experimental material. Comprehensive bioinformatic analysis was performed using ClustalX, MEGA, MEME, and PlantTFDB v5.0 to systematically characterize SRS family members within the wheat genome. The systematic examination of physicochemical properties, conserved domains, phylogenetic relationships, gene structures, and cis-acting elements was conducted, providing insights into the functional roles of this gene family in wheat growth and development. Fifteen SRS family members containing conserved zinc finger and IXGH domains were identified. Distinct expression patterns were observed among TaSRS subgroups: Members of Groups I, III, and V exhibited significantly higher transcript levels in roots, stems, leaves, and anthers compared to other subgroups. Notably, the majority of TaSRS genes, including representatives from Groups I, III, IV, and V, displayed responsiveness to NaCl and ABA stress treatments, suggesting their putative involvement in both salinity adaptation and phytohormone-mediated stress signaling. Differential expression patterns of TaSRS genes under NaCl and ABA stress were identified, revealing distinct regulatory impacts of these stressors on transcription. These findings establish a framework for investigating the molecular mechanisms underlying stress adaptation in wheat physiology. Full article

Background: Acyl-CoA oxidase (ACX), a ubiquitous eukaryotic enzyme, catalyzes the initial steps of fatty acid β oxidation and plays an important role in the biosynthesis of jasmonic acid (JA). At present, no studies have been reported on ACX family members of maize and their function in disease resistance. Objectives: This study aims to lay a foundation for clarifying the functions of ACX family genes in maize growth, development, and stress response by conducting a genome-wide identification of ACX family genes in maize, analyzing the expression characteristics of these genes in maize growth and development, hormone treatment and response to biotic and abiotic stresses, and exploring the functions of key genes in the maize disease resistance process through the use of mutants. Methods: ProtParam, TBtools, MEME, MEGA, and IBS tools were used to identify maize ACX family genes and analyze the physicochemical properties of their proteins, chromosome location, phylogenetic relationships among family members, conserved domains, conserved motifs, and cis-acting elements. Meanwhile, the expression patterns of maize ACX family genes in different tissues and their expression patterns under abiotic and biotic stresses were studied by using the data from the maize GDB database and qRT-PCR technology. Moreover, the mutants of ZmACX1, ZmACX3, ZmACX4, and ZmACX5 genes were obtained, and the disease resistance of the mutants was detected to further determine the functions of ACX genes in the maize disease resistance process. This study identified maize ACX family genes using bioinformatics methods. Results: We discovered that six ACX genes in the maize genome are distributed across four different chromosomes. Cluster analysis further classified these genes into three subfamilies. All maize ACX genes possess a conserved ACOX domain, and their promoter regions are enriched with cis-acting elements associated with heat stress and the plant hormone response. Under various tissue, biotic, and abiotic stress conditions, as well as treatments with methyl jasmonate (MeJA) and salicylic acid (SA), the expression levels of maize ACX family genes exhibited significant differences. Notably, the expression levels of ZmACX1, ZmACX3, ZmACX4, and ZmACX5 were significantly up-regulated following stress and pathogen infection, suggesting their involvement in maize growth, development, and disease resistance. To elucidate the function of these genes in maize disease resistance, the resistance of ZmACX1, ZmACX3, ZmACX4, and ZmACX5 mutants to Cochliobolus heterostrophus, Curvularia lunata, and Fusarium graminearum were further examined. The results revealed that compared to the wild-type B73, the lesion area of the mutants was significantly increased after inoculation with pathogens. This directly demonstrated the crucial role of these genes in maize resistance to C. heterostrophus, C. lunata, and F. graminearum. Conclusions: In summary, this study systematically identified maize ACX family genes, and thoroughly investigated their expression patterns and functions in maize disease resistance. Our findings provide valuable insights into the comprehensive understanding of the function and mechanism of maize ACX family genes. Full article

Background: Small heat shock proteins (sHsps), particularly Hsp20 family members, are pivotal for plant thermotolerance and abiotic stress adaptation. However, their evolutionary dynamics and functional roles in Lycium barbarum (goji berry), a commercially significant stress-tolerant crop, remain uncharacterized. This study aims to comprehensively identify LbHsp20 genes, delineate their evolutionary patterns, and decipher their regulatory mechanisms under heat stress to accelerate molecular breeding of resilient cultivars. Methods: Forty-three LbHsp20 genes were identified from the goji genome using HMMER and BLASTP. Phylogenetic relationships were reconstructed via MEGA-X (maximum likelihood, 1000 bootstraps), while conserved motifs and domains were annotated using MEME Suite and InterProScan. Promoter cis-elements were predicted via PlantCARE. Heat-responsive expression profiles of candidate genes were validated by qRT-PCR in two contrasting lines (N7 and 1402) under 42 °C treatment. Results: The LbHsp20 family clustered into 14 subfamilies, predominantly cytoplasmic (subfamilies I–VII). Chromosomal mapping revealed a tandem duplication hotspot on Chr4 (12 genes) and absence on Chr9, suggesting lineage-specific gene loss. All proteins retained the conserved α-crystallin domain (ACD), with 19 members harboring the ScHsp26-like ACD variant. Promoters were enriched in stress-responsive elements (HSE, ABRE, MYC). Heat stress induced significant upregulation (>15-fold in LbHsp17.6A and LbHsp18.3) in N7, whereas 1402 showed weaker induction (<5-fold). Subfamily specific divergence was observed, with cytoplasmic subfamily I genes exhibiting the strongest heat responsiveness. Conclusions: This study unveils the evolutionary conservation and functional diversification of LbHsp20 genes in L. barbarum. The tandem duplication-driven expansion on Chr4 and subfamily specific expression patterns underpin their roles in thermotolerance. These findings establish a foundation for engineering climate-resilient goji varieties. Full article

Dandelions possess a wide range of medicinal properties and demonstrate remarkable adaptability and tolerance to salinity and alkalinity. MYB genes in plants are implicated in growth, differentiation, metabolism, and responses to both biotic and abiotic stresses. The function of MYB genes in dandelions, particularly the R2R3-MYB gene family, requires further investigation. In this study, we identified a total of 130 members of the dandelion R2R3-MYB gene family at the genome-wide level, all of which were mapped to eight dandelion chromosomes. MEME analysis revealed that TmR2R3-MYB proteins contain three conserved motifs. Phylogenetic analysis categorized all TmR2R3-MYBs into 29 subfamilies. Transcriptomic studies in different tissues indicated that TmR2R3-MYBs exhibit distinct expression patterns in different tissues, indicating their diverse functions in dandelions. Notably, TmMYB44 from the S22 subfamily displayed the highest expression level in roots. Additionally, six representative TmR2R3-MYBs were selected from the S22 subfamily for expression profiling under salinity and alkalinity treatments. The results demonstrated that the TmR2R3-MYBs from the S22 subfamily are involved in the response to salinity and alkalinity stress. These findings provide a basis for further exploration of the functions of TmR2R3-MYBs in abiotic stress tolerance. Full article

The Dof gene family represents a class of plant-specific transcription factors that play crucial regulatory roles in various biological processes, including plant growth, development, and responses to abiotic stress. However, genome-wide identification and functional characterization of the Dof gene family remain unexplored in Dendrobium officinale. In this study, we performed a genome-wide identification and functional analysis of the DoDof gene family. A total of 28 Dof family members were identified and named DoDof1–28 based on genome annotation data. Phylogenetic analysis classified these genes into four major groups (A–D) and further subdivided them into nine subfamilies. Gene structure analysis revealed that most DoDofs lack introns, with no distinct specificity observed among different subfamilies and considerable diversity within the same subfamily. Sequence alignment analysis demonstrated that all DoDof proteins contain a conserved Dof domain consisting of 52 amino acids, which includes a C2-C2 zinc finger motif and a DNA-binding domain. MEME analysis revealed that the conserved motif composition exhibits a certain degree of conservation among DoDof proteins, but significant differences exist across subfamilies. Expression pattern analysis demonstrated that DoDofs have exhibited diverse expression profiles across different developmental stages, tissues, and under abiotic stresses (such as low temperature, salinity, and drought) in D. officinale, suggesting their potential roles in plant development and stress responses. Subcellular localization analysis indicated that DoDof15, DoDof22, and DoDof24 are localized exclusively in the nucleus. Yeast one-hybrid assays revealed that DoDof22 binds to the promoter of the ABA receptor DoPYL9, while DoDof15 and DoDof24 bind to the promoter of the bHLH transcription factor DobHLH68. These results suggest that DoDof proteins may regulate the growth, development, and stress response processes of D. officinale by binding to the promoters of target genes. This study provides critical insights into the functional roles of Dof transcription factors in Orchidaceae family and establishes a theoretical foundation for molecular breeding and stress resistance improvement in D. officinale. Full article

Background: The NAC transcription factor family of genes is one of the largest families of transcription factors in plants, playing important functions in plant growth and development, response to adversity stress, disease resistance, and hormone signaling. In this study, we identified the number of members of the Panax notoginseng NAC (PnNAC) gene family and conducted a comprehensive analysis of their physicochemical characteristics, chromosomal location, evolutionary features, and expression patterns both in different parts of the plant at different growth stages and in response to infection by Alternaria panax. Methods: The NAC gene family in P. notoginseng was identified using Hidden Markov Model (HMMER) and National Center of Biotechnology Information Conserved Domain Database (NCBI CDD), and their physicochemical properties were analyzed with Perl scripts. Phylogenetic relationships were determined using Clustal Omega and FastTree, and gene structures were visualized with an R script. Promoter regions were analyzed with PlantCARE, motifs with MEME and ggmotif, and transcriptome data were processed using Hical Indexing for Spliced Alignment of Transcripts (HISAT2) and HTseq. Results: This study identified 98 PnNAC genes in P. notoginseng, analyzed their characteristics (protein lengths 104–882 aa, molecular weights 11.78–100.20 kDa, isoelectric points 4.12–9.75), location (unevenly distributed on 12 chromosomes, no tandem repeats), evolution, and expression patterns (distinct in different parts, growth stages, and after A. panax infection). Conclusions: PnNAC plays an important role in the growth and development of P. notoginseng and in its response to A. panax. PnNAC could be a candidate gene for further research on and functional analysis of P. notoginseng disease resistance. Full article

Sugars will eventually be exported transporter (SWEET), a class of glucose transport proteins, is crucial in plants for glucose transport by redistribution of sugars and regulates growth, development, and stress tolerance. Although the SWEET family has been studied in many plants, little is known about its function in winter B. rapa (Brassica rapa L.). Bioinformatics approaches were adopted to identify the SWEET gene (BraSWEETs) family in B. rapa to investigate its role during overwintering. From the whole-genome data, 31 BraSWEET genes were identified. Gene expansion was realized by tandem and fragment duplication, and the 31 genes were classified into four branches by phylogenetic analysis. As indicated by exon–intron structure, cis-acting elements, MEME (Multiple EM for Motif Elicitation) motifs, and protein structure, BraSWEETs were evolutionarily conserved. According to the heat map, 23 BraSWEET genes were differentially expressed during overwintering, revealing their potential functions in response to low-temperature stress and involvement in the overwintering memory-formation mechanism. BraSWEET10 is mainly associated with plant reproductive growth and may be crucial in the formation of overwintering memory in B. rapa. The BraSWEET10 gene was cloned into B. rapa (Longyou-7, L7). The BraSWEET10 protein contained seven transmembrane structural domains. Real-time fluorescence quantitative PCR (qRT-PCR) showed that the BraSWEET10 gene responded to low-temperature stress. BraSWEET10 was localized to the cell membrane. The root length of overexpressing transgenic A. thaliana was significantly higher than that of wild-type (WT) A. thaliana under low temperatures. Our findings suggest that this gene may be important for the adaptation of winter B. rapa to low-temperature stress. Overall, the findings are expected to contribute to understanding the evolutionary links of the BraSWEET family and lay the foundation for future studies on the functional characteristics of BraSWEET genes. Full article

Serine acetyltransferase (SAT) is a critical enzyme in the sulfur-assimilation pathway of cysteine, playing an essential role in numerous physiological functions in plants, particularly in their response to environmental stresses. However, the structural characteristics of the soybean SAT gene family remain poorly understood. Members of the soybean SAT gene family were identified using the Hidden Markov Model approach. Bioinformatics tools, such as ExPASy, PlantCARE, MEME, and TBtools-II, were employed to examine the physicochemical properties, cis-regulatory elements, conserved motifs, gene structures, and chromosomal positions of the GmSAT genes. RT-qPCR was conducted to evaluate the expression profiles of GmSAT genes under NaCl-induced stress, identifying genes likely involved in the salt-stress response. A total of ten GmSAT genes were identified in the soybean genome and grouped into three subfamilies. Genes within each subfamily shared notable structural similarities and conserved motifs. Analysis of cis-regulatory elements revealed that the promoters of these genes contain several elements linked to plant growth and stress-related responses. Expression patterns of GmSAT genes varied across different soybean tissues, with GmSAT10 showing higher expression in roots, while GmSAT1 and GmSAT2 had lower expression in the same tissue. Following NaCl treatment, expression levels of seven GmSAT genes were significantly increased in the roots, indicating their potential involvement in the plant’s adaptation to salt stress. GmSAT genes appear to play crucial roles in soybean’s response to salt stress, offering insights that could aid in the development of salt-tolerant soybean varieties. Full article

The Mediator complex (MED) functions as a co-activator in plants, transmitting transcriptional signals to regulate gene expression, including responses to environmental stresses. While the MED gene family has been identified in several species, it has not yet been reported in cassava. In this study, we identified 32 members of the MeMED gene family in cassava (Manihot esculenta Crantz) distributed across 13 chromosomes. These genes were categorized into distinct Mediator subunits based on their similarity to Arabidopsis modules. Promoter analysis revealed the presence of various cis-regulatory elements, which likely play key roles in regulating plant growth, development, and stress responses. RNA-seq data showed tissue-specific expression patterns for the MeMED genes, with significant expression observed in leaves, roots, petioles, stems, friable embryogenic callus, and shoot apical meristems. Further RT-qPCR analysis under various abiotic stress conditions—including drought, exogenous hydrogen peroxide, cold, heat, and salt—demonstrated that 10 selected MeMED genes exhibited significant differential expression, indicating their potential functional involvement in stress adaptation. These findings offer insights into the biological roles of the MeMED gene family in cassava, with implications for improving stress tolerance in future breeding programs. Full article

Comparative analysis based on the mitogenomes of hares in Xinjiang, China, is limited. In this study, the complete mitochondrial genomes of seven hare samples including four hare species and their hybrids from different environments were sequenced, assembled, and annotated. Subsequently, we performed base content and bias analysis, tRNA analysis, phylogenetic analysis, and amino acid sequence analysis of the annotated genes to understand their characteristics and phylogenetic relationship. Their mitogenomes are circular molecules (from 16,691 to 17,598 bp) containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region, which are similar with other Lepus spp. worldwide. The relative synonymous codon usage analysis revealed that the adaptation of Lepus yarkandensis to its unique arid and hot environment might be associated with synthesizing amino acids like alanine, leucine, serine, arginine, and isoleucine and the terminator caused by the different usage of codons. Further, we utilized the MEME model and identified two positive selection genes (ND4, ND5) in Lepus tibetanus pamirensis and one (ND5) in L. yarkandensis that might be important to their adaptation to the plateau and dry and hot basin environments, respectively. Meanwhile, Lepus tolai lehmanni and Lepus timidus may have evolved different adaptive mechanisms for the same cold environment. This study explored the evolutionary dynamics of Xinjiang hares’ mitochondrial genomes, providing significant support for future research into their adaptation mechanisms in extreme environments. Full article

Building on my recent argument that an all-good, all-powerful God is logically incompatible with all the evil in the world, I explore what grounding ethics can have without the God of traditional theism. While theists have argued that ethics is grounded either in God’s commands and/or in his nature, I show that no such adequate grounding exists, even if my argument—showing that the God of traditional theism is logically incompatible with all the evil in the world—were shown to be unsuccessful, and I further show that such a grounding is impossible, given that my argument is successful. I then go on to provide an account of the norms on which an ethics without God can be appropriately grounded and show how an ethics, so grounded, can be appropriately related to our biological and cultural past, present, and future, as understood through Darwinian evolutionary theory. In this way, I hope to undercut a recent attempt to use Darwinian evolutionary theory to debunk ethics. Full article

Acinetobacter baumannii is a major cause of nosocomial infections, and its highly adaptive nature and broad range of antibiotic resistance enable it to persist in hospital environments. A. baumannii often employs two-component systems (TCSs) to regulate adaptive responses and virulence-related traits. This study describes a previously uncharacterized TCS in the A. baumannii ATCC19606 strain, consisting of a transcriptional sensor, DJ41_1407, and its regulator, DJ41_1408, located adjacent to GacA of the GacSA TCS. Markerless mutagenesis was performed to construct DJ41_1407 and DJ41_1408 single and double mutants. DJ41_1408 was found to upregulate 49 genes and downregulate 43 genes, most of which were associated with carbon metabolism and other metabolic pathways, such as benzoate degradation. MEME analysis revealed a putative binding box for DJ41_1408, 5′TGTAAATRATTAYCAWTWAT3′. Colony size, motility, biofilm-forming ability, virulence, and antibiotic resistance of DJ41_1407 and DJ41_1408 single and double mutant strains were assessed against wild type. DJ41_1407 was found to enhance motility, while DJ41_1408 was found to upregulate biofilm-forming ability, and may also modulate antibiotic response. Both DJ41_1407 and DJ41_1408 suppressed virulence, based on results from a G. mellonella infection assay. These results showcase a novel A. baumannii TCS involved in metabolism, with effects on motility, biofilm-forming ability, virulence, and antibiotic response. Full article

SARS-CoV-2 amino acid variants that contribute to an increased transmissibility or to host immune system escape are likely to increase in frequency due to positive selection and may be identified using different methods, such as codeML, FEL, FUBAR, and MEME. Nevertheless, when using different methods, the results do not always agree. The sampling scheme used in different studies may partially explain the differences that are found, but there is also the possibility that some of the identified positively selected amino acid sites are false positives. This is especially important in the context of very large-scale projects where hundreds of analyses have been performed for the same protein-coding gene. To account for these issues, in this work, we have identified positively selected amino acid sites in SARS-CoV-2 and 15 other coronavirus species, using both codeML and FUBAR, and compared the location of such sites in the different species. Moreover, we also compared our results to those that are available in the COV2Var database and the frequency of the 10 most frequent variants and predicted protein location to identify those sites that are supported by multiple lines of evidence. Amino acid changes observed at these sites should always be of concern. The information reported for SARS-CoV-2 can also be used to identify variants of concern in other coronaviruses. Full article

Verpa spp. are potentially important economic fungi within Morchellaceae. However, fundamental research on their mating systems, the key aspects of their life cycle, remains scarce. Fungal sexual reproduction is chiefly governed by mating-type genes, where the configuration of these genes plays a pivotal role in facilitating the reproductive process. For this study, de novo assembly methodologies based on genomic data from Verpa spp. were employed to extract precise information on the mating-type genes, which were then precisely identified in silico and by amplifying their single-ascospore populations using MAT-specific primers. The results suggest that the MAT loci of the three tested strains of V. bohemica encompassed both the MAT1-1-1 and MAT1-2-1 genes, implying homothallism. On the other hand, amongst the three V. conica isolates, only the MAT1-1-1 or MAT1-2-1 genes were present in their MAT loci, suggesting that V. conica is heterothallic. Moreover, bioinformatic analysis reveals that the three tested V. bohemica strains and one V. conica No. 21110 strain include a MAT1-1-10 gene in their MAT loci, while the other two V. conica strains contained MAT1-1-11, exhibiting high amino acid identities with those from corresponding Morchella species. In addition, MEME analysis shows that a total of 17 conserved protein motifs are present among the MAT1-1-10 encoded protein, while the MAT1-1-11 protein contained 10. Finally, the mating type genes were successfully amplified in corresponding single-ascospore populations of V. bohemica and V. conica, further confirming their life-cycle type. This is the first report on the mating-type genes and mating systems of Verpa spp., and the presented results are expected to benefit further exploitation of these potentially important economic fungi. Full article

The authors of this article advocate the view that the transformation from a physics paradigm to an informatics paradigm is not a denial of the effectiveness and scope of application of the physics paradigm, but a criticism of the “arrogance” of the physics paradigm, which misleads research in the humanities and social sciences. Through the “disciplinary informatization” of the humanities and social sciences, their own disciplinary paradigms can be established. The research objects of “communication” and “dissemination”, respectively, are “material” and “information”, meaning that they should follow different scientific paradigms. After achieving the transformation into an informatics paradigm, we should strive to explore the “cooperation” between the two paradigms, allowing them to explain “nature” (such as biological gene DNA) and “society” (cultural gene MEME), especially human “thinking”. Obviously, the conditions for solving “physical and mental problems” since Plato and Descartes have already been met. Full article