Search Results (310)

The WRKY gene family comprises important transcription factors widely distributed in plants and plays significant roles in the growth and development, diverse (biotic and abiotic) stress responses, and various biological processes. In the current study, 96 identified HvLWRKY genes were classified into three groups and seven subgroups. Among these, 89 genes possessed the conserved domain WRKYGQK. A total of ten motifs were harbored in HvLWRKY genes with two to four introns. Fragmental duplication was suggested to be the prime force that drove the evolution of HvLWRKY genes. A high degree of collinearity was observed between barley and Triticum spelta. Cis-elements of HvLWRKYs were closely associated with abiotic stress, light response, and hormone response; however, there were differences in the numbers among groups. HvLWRKY genes, even the paralogous gene pairs, from different clades were differentially regulated under cold treatments in two landraces. HvLWRKY33, 43, 44, 57, 65, and 77 were homologous with the relative AtWRKY genes in Arabidopsis thaliana. They are suggested to regulate abiotic and pathogen resistance of two barley landraces via SA and JA pathways. Meanwhile, some genes (for example, HvLWRKY1 and HvLWRKY32) were specifically expressed in either cold-tolerant or cold-sensitive landraces. Under cold stress, different cold-responsive patterns occurred in different barley landraces. These findings provide a foundation for further studies on cold resistance in barley landraces and offer new insights for application of WRKY genes in barley breeding. Full article

The role of G-quadruplexes (G4s) in gene regulation has been widely documented, especially in gene promoters. However, the transcriptional mechanisms involving G4s in other regulatory regions remain largely unexplored. In this study, we integrated the G4-DNA data derived from 22 breast cancer patient-derived tumor xenograft (PDTX) models and MCF7 cell line as potential breast cancer-associated G4s (BC-G4s). Genome-wide analysis showed that BC-G4s are more prevalent in gene promoters and the first introns. The genes accommodating promoter or intronic BC-G4s show significantly higher transcriptional output than their non-G4 counterparts. The biased distribution of BC-G4s in close proximity to the transcription start site (TSS) is associated with an enrichment of transcription factor (TF) interactions. A significant negative correlation was detected between the G4–TF interactions within the first introns and their cognate promoters. These different interactions are complementary rather than redundant. Furthermore, the differentially expressed genes (DEGs) harboring promoter and first intron BC-G4s are significantly enriched in the cell cycle pathway. Notably, promoter BC-G4s of DEGs could be a central hub for TF–TF co-occurrence. Our analysis also revealed that G4-related single nucleotide variants (SNVs) affect the stability of G4 structures and the transcription of disease-related genes. Collectively, our results shed light on how BC-G4s within promoters and first introns regulate gene expression and reinforce the critical role of G4s and G4-related genes in breast cancer-associated processes. Full article

The core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. However, research on the genetic characteristics within this breed and the genes associated with athletic performance remains relatively limited. We conducted whole-genome resequencing of Grassland-Thoroughbred F1, F2, F3, and the crossbred population (CY) and obtained a total of 4056.23 Gb of high-quality data after quality control. The single nucleotide polymorphisms (SNPs) were primarily distributed in intergenic regions, followed by intronic regions. Principal component analysis (PCA) and STRUCTURE revealed clear distinctions among the generations, with a notable overlap between CY and F3. Using the SNP dataset, we analyzed the number and length distribution patterns of runs of homozygosity (ROHs) in the genomes of different generational groups of Grassland-Thoroughbreds. Short ROHs ranging from 0.5 to 2 Mb were the most abundant, with the following distribution: F1 (85.15%) > F2 (82.92%) > CY (78.75%) > F3 (77.51%). Medium-length ROHs (2–8 Mb) and long ROHs (>8 Mb) together exhibited a similar but opposite trend. The average length of ROHs was 1.57 Mb. The inbreeding coefficients (F_ROH) among different generational groups of Grassland-Thoroughbreds were as follows: F1 (0.0942) < F2 (0.1197) < CY (0.1435) < F3 (0.1497). Through ROH island analysis, 10 high-frequency ROH regions were identified and annotated with 120 genes. Genomic regions and candidate genes associated with athletic traits—ACAD8, OPCML, PRDX2, NTM, NDUFB7, SCL25A15, FOXO1, and SLC4A10—were identified. These genes may play important roles in regulating muscle performance, mitochondrial energy supply, and learning and memory processes in horses and are closely associated with the athletic ability of the Grassland-Thoroughbred population. This study is the first to systematically characterize the genomic diversity and inbreeding dynamics of the Grassland-Thoroughbred during the breeding process. It identifies candidate genes that may influence athletic performance, thereby providing an important molecular foundation and theoretical basis for the genetic improvement and performance-based selection of this emerging breed. Full article

Plant protein phosphatase 2C (PP2C) represents the largest and most functionally diverse group of protein phosphatases in plants, playing pivotal roles in regulating metabolic processes, hormone signaling, stress responses, and growth regulation. Despite its significance, a comprehensive genome-wide analysis of the PP2C gene family in oat (Avena sativa L.) has remained unexplored. Leveraging the recently published oat genome, we identified 194 AsaPP2C genes, which were unevenly distributed across all 21 chromosomes. A phylogenetic analysis of PP2C classified these genes into 13 distinct subfamilies (A-L), with conserved motif compositions and exon-intron structures within each subfamily, suggesting evolutionary functional specialization. Notably, a promoter analysis revealed an abundance of stress-responsive cis-regulatory elements (e.g., MYB, MYC, ARE, and MBS), implicating AsaPP2Cs in hormones and biotic stress adaptation. To elucidate their stress-responsive roles, we analyzed transcriptomic data and identified seven differentially expressed AsaPP2C (Asa_chr6Dg00217, Asa_chr6Ag01950, Asa_chr3Ag01998, Asa_chr5Ag00079, Asa_chr4Cg03270, Asa_chr6Cg02197, and Asa_chr7Dg02992) genes, which were validated via qRT-PCR. Intriguingly, these genes exhibited dynamic expression patterns under varying stress conditions, with their transcriptional responses being both time-dependent and stress-dependent, highlighting their regulatory roles in oat stress adaptation. Collectively, this study provides the first comprehensive genomic and functional characterization of the PP2C family in oat, offering valuable insights into their evolutionary diversification and functional specialization. Full article

This study performed a phylogenomic analysis of the C2H2 gene family across 30 Basidiomycota species, identifying 1032 genes distributed across six evolutionary clades (Groups I–VI). Functional diversification and lineage-specific expansions were observed: Group II (37.1%) formed a conserved core, while wood decayers (e.g., Schizophyllum commune) and edible fungi (e.g., Pleurotus ostreatus) exhibited clade-specific expansions in Groups III and V, respectively. Physicochemical profiling revealed an acidic bias in Agaricomycotina proteins (pI 4.3–5.8) compared to alkaline trends in pathogens (Ustilaginomycotina/Pucciniomycotina; pI 8.3–8.6). Comparative genomics indicated that saprotrophs retained long genes (12.4 kb) with abundant introns (mean = 6.2/gene), whereas pathogens exhibited genomic streamlining (introns ≤ 2). Synteny network analysis revealed high ancestral conservation in core clusters (Cluster_1–2: 58% homologs) under strong purifying selection (Ka/Ks = 0.18–0.22), while peripheral clusters (Cluster_Mini) approached neutral evolution (Ka/Ks = 0.73). This study reveals stage-specific expression dynamics of 17 C2H2 zinc finger genes in Sarcomyxa edulis, highlighting their roles in coordinating developmental transitions (e.g., SeC2H2_1 in low-temperature adaptation, SeC2H2_7/12 in primordia initiation, and SeC2H2_8/9/13 in fruiting body maturation) through temporally partitioned regulatory programs, providing insights into fungal morphogenesis and stress-responsive adaptation. These findings underscore the dual role of C2H2 genes in sustaining conserved regulatory networks and facilitating ecological adaptation, providing new insights into fungal genome evolution. Full article

The DOG1 (Delay of Germination1) family plays key regulatory roles in seed dormancy and germination. However, a genome-wide analysis of DOG1 genes has not been performed for pepper (Capsicum annuum), one of the agriculturally important species, and no studies have been conducted to characterize their expression profiles. Based on C. annuum genome information, the identification and expression analysis of CaDOG1 gene family members through bioinformatics approaches can provide a theoretical foundation for subsequent studies on the biological functions of CaDOG1s and the improvement of seed traits in C. annuum breeding. In this study, a total of 13 CaDOG1 genes were identified in the C. annuum genome. Phylogenetic analysis showed that these CaDOG1s, along with DOG1s from thale cress (Arabidopsis thaliana), rice (Oryza sativa), and maize (Zea mays), were classified into four subgroups. All CaDOG1 genes were unevenly distributed on six C. annuum chromosomes, and they had relatively conserved exon–intron patterns, most with zero to one intron. According to the chromosomal distribution patterns and synteny analysis of the CaDOG1 genes, the CaDOG1 family expanded mainly through replication, which occurred predominantly after the divergence of dicotyledons and monocotyledons. Conserved motif analysis indicated that all encoded proteins contained Motif 2 and Motif 6, except for CaDOG1-3. Expression profile analysis using transcriptome data revealed that CaDOG1 genes were differentially expressed across various tissues and developmental stages, with notable involvement in flowers and seeds. Quantitative real-time PCR also revealed that all CaDOG1 genes were downregulated during seed germination, indicating that CaDOG1s may play negative roles in seed germination. Moreover, upon abscisic acid treatment, six CaDOG1 genes exhibited upregulation, while in response to ethylene, four CaDOG1 genes exhibited downregulation. Taken together, these findings provide an extensive description of the C. annuum DOG1 gene family and might facilitate further studies for elucidating their functions in seed germination. Full article

Background: Genetic variation provides a foundation for understanding evolution. With the rise of artificial intelligence, machine learning has emerged as a powerful tool for identifying genomic footprints of evolutionary processes through simulation-based predictive modeling. However, existing approaches require prior knowledge of the factors shaping genetic variation, whereas uncovering anomalous genomic regions regardless of their causes remains an equally important and complementary endeavor. Methods: To address this problem, we introduce ANDES (ANomaly DEtection using Summary statistics), a suite of algorithms that apply statistical techniques to extract features for unsupervised anomaly detection. A key innovation of ANDES is its ability to account for autocovariation due to linkage disequilibrium by fitting curves to contiguous windows and computing their first and second derivatives, thereby capturing the “velocity” and “acceleration” of genetic variation. These features are then used to train models that flag biologically significant or artifactual regions. Results: Application to human genomic data demonstrates that ANDES successfully detects anomalous regions that colocalize with genes under positive or balancing selection. Moreover, these analyses reveal a non-uniform distribution of anomalies, which are enriched in specific autosomes, intergenic regions, introns, and regions with low GC content, repetitive sequences, and poor mappability. Conclusions: ANDES thus offers a novel, model-agnostic framework for uncovering anomalous genomic regions in both model and non-model organisms. Full article

The genetic diversity of cattle plays a crucial role in adapting to environmental challenges and enhancing production traits. While research has predominantly focused on single nucleotide polymorphisms (SNPs), small indel and structural variants (SVs) also significantly contribute to genetic variation. This study investigates the distribution and functional impact of insertions and deletions in five Hubei indigenous cattle breeds. A total of 3,208,816 deletions and 2,082,604 insertions were identified, with the majority found in intergenic and intronic regions. Hotspot regions enriched in immune-related genes were identified, underscoring the role of these variants in disease resistance and environmental adaptation. Our analysis revealed a strong influence of transposable elements (TEs), particularly LINEs and SINEs, on genomic rearrangements. The variants were also found to overlap with economically important traits, such as meat quality, reproduction, and immune response. Population structure analysis revealed genetic differentiation among the breeds, with Wuling cattle showing the highest differentiation. Notably, the NOTCH2 gene was identified as a candidate for regional adaptation due to its significant differentiation across populations. These findings provide valuable genomic resources for enhancing breeding programs, aiming at improving the productivity and resilience of indigenous cattle breeds in China. Full article

SABATH methyltransferase can methylate small-molecule metabolites of plants to generate different products, and it plays a crucial role in plant growth and development as well as stress response. In this study, 13 SABATH genes distributed on five chromosomes of cucumbers were identified, and the synergistic effects among their domains, gene structures, conserved motifs, phylogenetic relationships, collinearity analysis, cis-acting elements, expression patterns, and plant growth-promoting rhizosphere bacteria (PGPR) were analyzed. The gene structure and conserved motifs of the same group of CsSABATH have similar intron numbers and conserved motifs. We detected 10 cis-elements in the promoter of the CsSABATH gene, indicating that they may be involved in different signaling pathways. qRT-PCR revealed the tissue-specific, drought and salt stress-responsive expression of the SABATH gene in cucumbers. Furthermore, we also verified that the expression level of CsaV3_6G046510 after inoculation with PGPR-GD17 bacteria under drought and salt stress was significantly lower than normal drought and salt dress, indicating that this gene may respond to PGPR and in abiotic stress play an important role. This study provides valuable insights into the molecular characteristics and evolutionary history of the SABATH gene family in cucumbers, laying a foundation for further analysis of the function of the CsSABATH gene in cucumbers. Full article

UDP-glycosyltransferases (UGTs) are widely distributed enzymes in living organisms that catalyze the transfer of glycosyl groups from donor molecules to acceptor molecules’ glycoside ligands. These enzymes are pivotal for detoxifying and eliminating both endogenous and exogenous toxic substances in insects. In this study, bioinformatics methods were used to analyze the UGT gene superfamily in the fall armyworm (Spodoptera frugiperda), resulting in the identification of 48 UGT genes located across 10 chromosomes, including 23 tandem duplication pairs. The predicted SfUGT proteins mainly exhibit α-helical secondary structures. Intron numbers varied significantly, with high diversity observed in amino acid sequences. Phylogenetic analysis grouped UGT genes from three insect species into three distinct subfamilies, revealing a closer evolutionary relationship between S. frugiperda and Spodoptera litura, supported by a greater number of orthologous genes. Expression profiling showed that SfUGT16 and SfUGT21 are highly expressed in the first and fourth larval instars, respectively; SfUGT16 is predominantly expressed in the Malpighian tubules and midgut, implying roles in digestion, metabolism, and detoxification. Meanwhile, SfUGT21, SfUGT30, and SfUGT48 exhibited elevated expression in the hemolymph, suggesting functions in metabolism and transport, whereas SfUGT40 showed high expression in both the midgut and hemolymph, indicating involvement in detoxification and metabolic processes. These findings provide a foundation for further exploration of the biological functions of the UGT gene family. Full article

The U-box E3 ubiquitin ligase (PUB) gene family plays an important role in regulating plant responses to abiotic stress. Poncirus trifoliata (trifoliate orange), a citrus rootstock with notable cold, drought, and salt tolerance, serves as an excellent model for studying stress-responsive genes. In this study, a total of 47 PUB genes (PtrPUBs) were identified in the trifoliate orange genome. Chromosomal distribution analysis indicated that PtrPUB genes were unevenly distributed across nine trifoliate orange chromosomes. Phylogenetic tree analysis indicated that 170 PUB proteins from trifoliate orange, Arabidopsis thaliana, and tomato were clustered into five subfamilies. Gene structure, conserved domain, and motif analyses revealed diverse exon–intron and motif organizations of PtrPUB genes, suggesting potential functional differentiation among PtrPUBs. Cis-acting analysis indicated that the promoters of PtrPUB genes harbor elements related to hormone signaling (ABA, MeJA), drought stress, and low-temperature responses. Transcriptomic data and qRT-PCR results suggested that PtrPUB genes are responsive to ABA and dehydration treatments. This study provides a foundation for understanding the functional roles of PUB genes in trifoliate orange and offers insights for improving stress tolerance in citrus breeding programs. Full article

Phoebe bournei, a rare tree species native to China, holds considerable economic importance. The heat shock protein 70 (Hsp70) family is a group of molecular chaperones that is broadly distributed across living organisms and play a critical role in processes like growth, development, and stress response. While Hsp70 genes have been identified and studied in various plant species, their specific functions in the growth and development of P. bournei remain unexplored. We performed a comprehensive analysis of the Hsp70 gene family in P. bournei, identifying a total of 45 Hsp70 genes, which were classified into four groups (I–IV) through phylogenetic analysis. All Hsp70 proteins possessed conserved structural domains, including motif 7, and introns were present in 77.8% of the genes. Chromosomal localization and collinearity analyses of the Hsp70 genes revealed their evolutionary relationships and potential gene duplication events. Examination of the cis-acting elements within the Hsp70 promoter regions revealed that the predominant elements were associated with growth and development, followed by those responsive to hormones, and then elements linked to abiotic stress. Nine genes with high expression were selected for RT-qPCR analysis. Under high-temperature stress, all nine genes were differentially upregulated, and most of these genes belonged to subfamilies II and III, indicating that these two subfamilies have strong potential for heat resistance. In this study, we have elucidated the molecular characteristics and heat response properties of the Hsp70 gene family in P. bournei, revealing the mechanisms behind its heat stress response. Our work provides a reference for stress breeding in P. bournei and a theoretical basis for the exploration of heat tolerance in woody plants. Full article

Severe physiological fruit abscission significantly limits yield potential in macadamia. Polygalacturonase (PG), a key hydrolytic enzyme in pectin degradation, plays a critical role in fruit abscission. However, in the macadamia genome, the PG gene family and the members involved in fruit abscission remain poorly understood. In this study, 56 PG gene family members, which were unevenly distributed across 13 of the 14 chromosomes, were identified in the macadamia genome. Phylogenetic analysis clustered these genes into seven clades, with most members found in clades D and E. The MiPGs contained 3–11 exons and 2–10 introns, and except for those in clades E and G, most contained conserved domains I–IV and were predicted to be localized exclusively to the cell membrane. MiPG promoter analysis revealed numerous light-, phytohormone-, and stress-responsive cis-elements. Expression profiling during fruit development showed that twelve MiPGs were either undetectable or expressed at low levels in the fruit abscission zone, whereas eight were highly expressed. MiPG9, MiPG37, and MiPG53 were significantly upregulated during abscission induced by a combination of girdling with defoliation and ethephon treatments. Moreover, transient MiPG37 overexpression in lily petals promoted premature abscission, suggesting that this gene plays a pivotal role in macadamia fruit abscission. These findings advance the functional characterization of macadamia PG genes and highlight a subset of candidate genes for further genetic manipulation to improve fruit retention. Full article

Plant cuticular wax serves as a critical component for defense against biotic and abiotic stresses, with its biosynthetic pathway regulated by the ECERIFERUM (CER) gene family. This study presents the first genome-wide identification of 79 CER genes (CalCERs) in pepper (Capsicum annuum L.), which are distributed across all 12 chromosomes. Phylogenetic analysis classified CalCERs into five clades, with clade-specific conservation of exon–intron architectures and protein motifs. Promoter cis-element analysis revealed enrichment of light-responsive elements, abscisic acid (ABA), jasmonic acid (JA), and stress-responsive regulatory motifs, indicating multi-pathway regulation. Transcriptomic data highlighted tissue-specific expression patterns, such as the root-predominant express gene CalCER1-2 and the flower-specific express gene CalCER3-1. Under abiotic stresses (drought, salt, heat, and cold), CalCER4-2 and CalCER6-6 responded rapidly, while most genes showed delayed differential expression. Under biotic stress, CalCER3-1 and CalCER5-3 were upregulated, whereas CalCER2-2 exhibited pathogen-specific suppression, suggesting roles in modulating wax-mediated pathogen resistance. Hormone treatments revealed dynamic responses: CalCER2-2 was persistently ABA-inducible, while CalCER3-1 specifically responded to JA. This study underscores evolutionary conservation and species-specific expansion of the pepper CER family, linking their expression to wax biosynthesis and stress adaptation. These insights provide a foundation for enhancing stress resilience in crops. Future work should employ gene editing and metabolomics to validate functional mechanisms and optimize breeding strategies. Full article

Transposable elements (TEs) are major drivers of plant genome plasticity, but the immediate molecular consequences of new TE insertions remain poorly understood. In this study, we generated a wild-type Arabidopsis thaliana population with novel insertions of ONSEN retrotransposon to investigate early epigenomic and transcriptomic changes using whole-genome and cDNA nanopore sequencing. We found that novel ONSEN insertions were distributed non-randomly, with a strong preference for genic regions, particularly in chromatin enriched for H2A.Z, H3K27me3, and H3K4me2. Most full-length ONSEN insertions within genes were rapidly recognized and spliced out as new introns (intronization), thereby mitigating potential deleterious effects on transcript isoforms. In some cases, ONSEN insertions provided alternative transcription start or termination sites, generating novel transcript isoforms. Genome-wide methylation analysis revealed that new ONSEN copies were efficiently and precisely targeted by DNA methylation. Independently on the location of the original ONSEN element, the euchromatic and heterochromatic insertions display distinct methylation signatures, reflecting the action of different epigenetic pathways. In conclusion, our results demonstrate that DNA methylation and alternative splicing are effective control mechanisms safeguarding the plant genome and transcriptome integrity after retrotransposition burst. Full article