Search Results (216)

Spondyloepimetaphyseal dysplasia type Isidor-Toutain (RPL13-SEMD) is an autosomal dominant skeletal dysplasia caused by heterozygous pathogenic variants in the RPL13 gene, encoding the ribosomal protein eL13. To date, 13 pathogenic variants in RPL13 have been reported, all clustering within intron 5 and exon 6, suggesting this hotspot region is critical for the function of ribosomes in skeletal tissues. Here, we present clinical and radiological characteristics of seven individuals, five children and two adults, from four unrelated families with RPL13-SEMD caused by two novel variants (c.477+5G>C and c.539_541del) and two previously reported variants (c.477+1G>C and c.548G>A) in RPL13. RNA analysis demonstrated that c.477+5G>C leads to a 54-nucleotide extension of exon 5, resulting in an 18-amino acid insertion. The phenotypic spectrum ranged from mild manifestations, such as Blount-like tibial deformity without significant short stature or Perthes-like femoral epiphyseal changes, to severe skeletal deformities with disproportionate short stature, accompanied by extraskeletal features (e.g., penoscrotal hypospadias, coccygeal abnormalities). For the first time, we describe Blount-like tibial deformity as a feature of this dysplasia, which resolves with age. Our study provides additional insights into the clinical, radiological, and genotypic features of RPL13-SEMD through detailed analysis of patients and their affected relatives. 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

Small heat shock proteins (sHsps) play crucial roles in organismal adaptation to stress tolerance. Sitodiplosis mosellana, a devastating insect wheat pest, undergoes long obligatory larval diapause to survive temperature extremes during summer and winter. To elucidate the function of sHsps in this process, two sHsp-encoding genes (SmHsp22.2 and SmHsp26.7) were characterized from S. mosellana, and their responsiveness to diapause and thermal stress, as well as their roles in cold stress, was analyzed. Both SmHsp22.2 and SmHsp26.7 possessed the canonical α-crystallin domain and lacked introns. Quantitative PCR indicated significant upregulation of SmHsp22.2 and SmHsp26.7 during diapause, especially in summer and winter. Notably, SmHsp22.2 exhibited higher expression in summer relative to winter, whereas SmHsp26.7 showed the opposite profile. Moreover, short-term heat shock (≥35 °C) in over-summering larvae or cold shock (≤−10 °C) in over-wintering larvae was found to trigger transcriptional upregulation of both genes, while prolonged temperature extremes (i.e., 45–50 °C or −15 °C) did not elicit a comparable response. RNA interference-mediated knockdown of both genes significantly increased the mortality of S. mosellana larvae under cold stress. These findings indicate the importance of both SmHsps in diapause and environmental adaptation in S. mosellana. Full article

Flower fragrance is a crucial ornamental and economic trait of Dendrobium chrysotoxum, and the most abundant and diverse aroma-active compounds are terpenes. Terpene synthase (TPS) is the ultimate enzyme for the biosynthesis of various types of terpenes, and TPS genes were identified as the key regulators governing the spatiotemporal release of volatile terpene compounds. Until recently, the TPS gene family in D. chrysotoxum has remained largely unexplored. Our study characterizes the TPS genes in D. chrysotoxum and identifies 37 DcTPS gene family members. It helped identify the DcTPS genes, gene characteristics, the phylogeny relationship, conserved motif location, gene exon/intron structure, cis-elements in the promoter regions, protein–protein interaction (PPI) network, tissue specific expression and verification of the expression across different flowering stages and floral organs. Three highly expressed DcTPS genes were cloned, and their functions were verified using a transient expressed in tobacco leaves. Further functional verification showed that the proteins encoded by these genes were enzymes involved in monoterpene synthesis, and they were all involved in the synthesis of linalool. This study comprehensively expatiates on the TPS gene family members in D. chrysotoxum for the first time. These data will help us gain a deeper understanding of both the molecular mechanisms and the effects of the TPS genes. Furthermore, the discovery that three TPS-b genes (DcTPS 02, 10, 32) specifically drive linalool-based scent in D. chrysotoxum, will provide new insights for expanding the TPS-b subfamily in orchids and identifying the linalool synthases contributing to orchid fragrance. Full article

Purple cowpea accumulates abundant anthocyanins in its epidermis, with R2R3-MYB transcription factors serving as potential regulators of anthocyanin accumulation. This study systematically deciphered the genome-wide characteristics of cowpea R2R3-MYB transcription factors, elucidating their critical roles in plant anthocyanin accumulation. Employing a combined strategy of HMMER Hidden Markov Model searches and BLASTP homology alignment, we successfully identified 127 non-redundant VuR2R3-MYB transcription factors. The encoded proteins exhibited remarkable physicochemical diversity: the average length reached 338.8 amino acid residues, with theoretical isoelectric points distributed between 4.79 and 10.91 residues. When performing a phylogenetic analysis with Arabidopsis homologs, 27 distinct subgroups were identified. Among them, the S4–S7 clades showed conserved protein architectures, which might play a role in regulating the phenylpropanoid pathway. An analysis of the gene architecture revealed patterns of intron/exon organization. Specifically, 85 out of 127 loci (66.9%) presented the typical two-intron configuration, whereas 18 genes had no introns. An investigation of the promoters found that, on average, each gene had 52 cis-regulatory elements. These elements were mainly light-responsive motifs and phytohormone-related elements. Chromosomal mapping indicated an uneven distribution of these genes across 11 chromosomes. Duplication analysis further showed 13 tandem repeats and 54 segmentally duplicated pairs. An analysis of evolutionary constraints demonstrated that purifying selection was predominant (Ka/Ks < 0.5) among paralogous pairs. Through comparative transcriptomics of pod color variants, 19 differentially expressed MYB regulators were identified. These included VuR2R3-MYB23 (MYB3 homolog), VuR2R3-MYB95 (MYB4 homolog), VuR2R3-MYB53 (MYB114 homolog), and VuR2R3-MYB92 (MYB5 homolog), which showed a strong correlation with the patterns of anthocyanin accumulation. Our findings are expected to contribute to elucidating the potential regulatory mechanisms through which R2R3-MYB transcription factors mediate anthocyanin biosynthesis and accumulation. Full article

The SWEET (Sugar Will Eventually be Exported Transporters) protein family plays a key role in plant growth, adaptation, and stress responses by facilitating soluble sugar transport. However, their functions in Cymbidium remain poorly understood. This study identified 59 SWEET genes across four Cymbidium species, encoding conserved MtN3/saliva domains. Despite variations in exon-intron structures, gene motifs and domains were highly conserved. Phylogenetic analysis grouped 95 SWEET proteins from six species into four clades, with gene expansion driven by whole-genome, segmental, and tandem duplications. Cis-element analysis and expression profiling across 72 samples revealed diverse regulatory patterns. Notably, SWEET genes showed peak expression in floral development, leaf morph variations, and diurnal rhythms. qRT-PCR and transcription factor binding analysis further highlighted their regulatory roles in floral patterning, leaf variation, and metabolic rhythms. These findings provide a foundation for future studies on SWEET gene function and their potential molecular breeding value in orchids. Full article

Mechanical injury to lettuce often leads to enzymatic browning caused by polyphenol oxidase (PPO), significantly impairing its sensory quality and processing suitability. In this study, the LsPPOs gene family was comprehensively identified and characterized using bioinformatics methods, including gene and protein structure, codon usage bias, phylogenetic relationships, and gene expression in response to wound stress. Further analysis of the relationship between LsPPOs expression profile and browning was performed. A total of 17 LsPPO family members (LsPPO1-LsPPO17) were identified from publicly available lettuce databases, encoding proteins ranging from 146 to 667 amino acids, with a G/C bias. Most were localized in the chloroplast. The motif structure was highly conserved among family members, and phylogenetic analysis revealed four distinct groups. All genes lacked introns, except LsPPO2 which contained an intron. After mechanical injury, browning at the stem site deepened over time, with PPO activity increasing. The majority of PPO members were significantly upregulated after fresh-cut processing. Among them, LsPPO3, LsPPO4, and LsPPO12 showed sustained upregulation, exhibiting a strong positive correlation with the browning phenotype and PPO activity. Notably, LsPPO4 demonstrated the highest transcriptional abundance and upregulation in response to a wound, indicating its major role in lettuce stem browning. The results of this study provide a foundation for further investigation into the functional role of LsPPOs and support the development of lettuce varieties with enhanced resistance to browning. Full article

Neonatal encephalopathy suspected to be due to hypoxic ischaemic encephalopathy (NESHIE) carries the risk of death or severe disability (cognitive defects and cerebral palsy). Previous genetic studies on NESHIE have predominantly focused on exomes or targeted genes. The objective of this study was to identify genetic variants associated with moderate–severe NESHIE through whole-genome, unbiased analysis. Variant filtering and prioritization were performed, followed by association testing both on a case–control basis and to compare the grades of severity and/or progression. Association testing on neonates with NESHIE (N = 172) and ancestry-matched controls (N = 288) produced 71 significant genetic variants (false discovery rate corrected p-value < 6.2 × 10⁻⁴), all located in non-coding regions and not previously implicated in NESHIE. Disease-associated variants in non-coding regions are considered to affect regulatory functions, possibly by modifying gene expression, promoters, enhancers, or DNA structure. The most significant variant was at position 6:162010973 in the Parkin RBR E3 ubiquitin protein ligase (PRKN) intron. Intronic variants were also identified in genes involved in inflammatory processes (SLCO3A1), DNA repair (ZGRF1), synaptogenesis (CNTN5), haematopoiesis (ASXL2), and the transcriptional response to hypoxia (PADI4). Ten variants were associated with a higher severity or lack of improvement in NESHIE, including one in ADAMTS3, which encodes a procollagen amino protease with a role in angiogenesis and lymphangiogenesis. This analysis represents one of the first efforts to analyze whole-genome data to investigate the genetic complexity of NESHIE in diverse ethnolinguistic groups of African origin and provides direction for further study. Full article

Isolated Growth Hormone Deficiency Type 2 (IGHD2) is caused by a heterozygous splice site variant in intron 3 of the GH1 gene. The resulting exon 3-skipped growth hormone (Δ3 GH), produced from the mutated allele, exerts a dominant-negative effect, leading to growth hormone (GH) deficiency. However, the precise molecular mechanisms underlying this effect remain poorly understood. While several model murine models expressing human Δ3 GH have been developed, no IGHD2 mouse models featuring variants in the endogenous Gh gene currently exist. We generated a mouse model (Gh^+/Δ3) with a heterozygous deletion of exon 3 in the Gh gene using CRISPR/Cas9 system. The Gh^+/Δ3 model exhibited GH deficiency caused by a dominant-negative effect at the mRNA level, characterized by reduced Gh mRNA expression. This mechanism parallels findings in our previous humanized IGHD2 mouse model, where the deficiency was driven by decreased Ghrhr mRNA expression. Transcriptome analysis of the pituitary revealed widespread downregulation of mRNAs encoding membrane and secretory proteins. The dominant-negative effect of Δ3 GH in IGHD2 is mediated by properties of Δ3 GH that are conserved across both humans and mice. This mechanism involves the downregulation of mRNAs, including those encoding membrane and secretory proteins, such as Ghrhr mRNA. Full article

Background/Objectives: Dermatophytosis, a prevalent fungal infection of keratinized tissues, is primarily caused by the filamentous fungus Trichophyton rubrum. Sertraline (SRT), an antidepressant with antifungal activity, has already demonstrated therapeutic potential against this fungus. Elucidating the effects of SRT may provide insights into its mechanism of action and fungal adaptation to this drug. Differential gene expression and alternative splicing (AS) facilitate fungal adaptations to various environmental conditions. This study aimed to provide a comprehensive overview of AS events and their implications in T. rubrum cultivated under sub-inhibitory concentrations of SRT. Method: The transcriptome of T. rubrum challenged with SRT was analyzed to detect AS events. Results: RNA-seq analysis revealed that SRT affected transcriptional and post-transcriptional events in numerous T. rubrum genes, including those encoding transcription factors, kinases, and efflux pumps. Among the AS events, intron retention was predominant. After 12 h of SRT exposure, intron-3 retention levels in the serine/arginine protein kinase mRNA transcripts were significantly increased compared with those in the control. This new isoform would produce a putative protein that partially lost its phosphotransferase domain. Conclusions: These findings highlight the potential mechanisms of action of SRT and suggest how T. rubrum adapts itself to this drug. Full article

Ustilago esculenta is a dimorphic fungus that specifically infects Zizania latifolia, causing stem swelling and the formation of an edible fleshy stem known as jiaobai. The pathogenicity of U. esculenta is closely associated with the development of jiaobai and phenotypic differentiation. Msb2 acts as a key upstream sensor in the MAPK (mitogen-activated protein kinase) signaling pathway, playing critical roles in fungal hyphal growth, osmotic regulation, maintenance of cell wall integrity, temperature adaptation, and pathogenicity. In this study, we cloned the UeMsb2 gene from U. esculenta (GenBank No. MW768949). The open reading frame of UeMsb2 is 3015 bp in length, lacks introns, encodes a 1004-amino-acid protein with a conserved serine-rich domain, and is localized to the vacuole. Expression analysis revealed that UeMsb2 is inducibly expressed during both hyphal growth and infection processes. Deletion of UeMsb2 did not affect haploid morphology or growth rate in vitro but significantly impaired the strain’s mating ability, suppressed filamentous growth, slowed host infection progression, and downregulated the expression of b signaling pathway genes associated with pathogenicity. Notably, the deletion of UeMsb2 did not influence the in vitro growth of U. esculenta under hyperosmotic, thermal, or oxidative stress conditions. These findings underscore the critical role of UeMsb2 in regulating the pathogenicity of U. esculenta. This study provides insights into the interaction between U. esculenta and Z. latifolia, particularly the mechanisms that drive host stem swelling. Full article

Trichoderma is a widely studied ascomycete fungal genus, including more than 400 species. However, genetic information on Trichoderma is limited, with most species reporting only DNA barcodes. Mitochondria possess their own distinct DNA that plays a pivotal role in molecular function and evolution. Here, we report 42 novel mitochondrial genomes (mitogenomes) combined with 18 published mitogenomes of Trichoderma. These circular mitogenomes exhibit sizes of 26,276–94,608 bp, typically comprising 15 core protein-coding genes (PCGs), 2 rRNAs, and 16–30 tRNAs; however, the number of endonucleases and hypothetical proteins encoded in the introns of PCGs increases with genome size enlargement. According to the result of phylogenetic analysis of the whole mitogenome, these strains diverged into six distinct evolutionary branches, supported by the phylogeny based on 2830 single-copy nuclear genes. Comparative analysis revealed that dynamic Trichoderma mitogenomes exhibited variations in genome size, gene number, GC content, tRNA copy, and intron across different branches. We identified three mutation hotspots near the regions encoding nad3, cox2, and nad5 that caused major changes in the mitogenomes. Evolutionary analysis revealed that atp9, cob, nad4L, nad5, and rps3 have been influenced by positive selection during evolution. This study provides a valuable resource for exploring the important roles of the genetic and evolutionary dynamics of Trichoderma mitogenome in the adaptive evolution of biocontrol fungi. Full article

A joint analysis of dendrochronological and genomic data was performed to identify genetic mechanisms of adaptation and assess the adaptive genetic potential of Siberian stone pine (Pinus sibirica Du Tour) populations. The data obtained are necessary for predicting the effect of climate change and mitigating its negative consequences. Presented are the results of an association analysis of the variation of 84,853 genetic markers (single nucleotide polymorphisms—SNPs) obtained by double digest restriction-site associated DNA sequencing (ddRADseq) and 110 individual phenotypic traits, including dendrophenotypes based on the dynamics of tree-ring widths (TRWs) of 234 individual trees in six natural populations of Siberian stone pine, which have a history of extreme climatic stresses (e.g., droughts) and outbreaks of defoliators (e.g., pine sawfly [Neodiprion sertifer Geoff.]). The genetic structure of studied populations was relatively weak; samples are poorly differentiated and belong to genetically similar populations. Genotype–dendrophenotype associations were analyzed using three different approaches and corresponding models: General Linear Model (GLM), Bayesian Sparse Linear Mixed Model (BSLMM), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), respectively. Thirty SNPs were detected by at least two different approaches, and two SNPs by all three. In addition, three SNPs associated with mean values of recovery dendrophenotype (Rc) averaged across multiple years of climatic stresses were also found by all three methods. The sequences containing these SNPs were annotated using genome annotation of a very closely related species, whitebark pine (P. albicaulis Engelm.). We found that most of the SNPs with supposedly adaptive variation were located in intergenic regions. Three dendrophenotype-associated SNPs were located within the 10 Kbp regions and one in the intron of the genes encoding proteins that play a crucial role in ensuring the integrity of the plant’s genetic information, particularly under environmental stress conditions that can induce DNA damage. In addition, we found a correlation of individual heterozygosity with some dendrophenotypes. Heterosis was observed in most of these statistically significant cases; signs of homeostasis were also detected. Although most of the identified SNPs were not assigned to a particular gene, their high polymorphism and association with adaptive traits likely indicate high adaptive potential that can facilitate adaptation of Siberian stone pine populations to the climatic stresses and climate change. Full article

Plant-specific APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factors are involved in the regulation of genes associated with the growth and developmental processes of numerous plants. Although AP2/ERF proteins from other species have been intensively studied, no studies have been reported on the AP2/ERF family of Luffa cylindrica, an important vegetable of the cucurbit family, and one of the most popular vegetables in the world. In this study, 133 genes (315–6696 bp) encoding LcAP2/ERF proteins with complete AP2/ERF domains were identified according to the luffa P93075 genome. These LcAP2/ERF genes were subsequently classified and analyzed for their gene structures, chromosomal distribution locations, promoter cis-acting elements, conserved structural domains of encoded proteins, and responses to abiotic stresses. The LcAP2/ERF genes were identified and divided into five phylogenetic groups (AP2, DREBs, ERFs, RAV, and soloists). These genes were unevenly distributed across 13 chromosomes. An analysis of gene structures indicated the LcAP2/ERF genes contained 0–11 introns (average of 4.4). Additionally, 16 motifs were identified in the LcAP2/ERF proteins that were conserved across different phylogenetic groups. Moreover, 11 cis-acting elements associated with response to the environment were analyzed in a 2000 bp region upstream of the LcAP2/ERF gene promoters. A transcriptome analysis involving RNA-seq data revealed tissue-specific LcAP2/ERF expression profiles and the diversity in LcAP2/ERF expression. The effects of low-temperature stress on LcAP2/ERF expression were determined. Furthermore, fruit-development-related and low-temperature-induced expressional changes were verified by RT-qPCR analyses of 14 differentially expressed LcAP2/ERF genes in luffa. Our findings will help clarify the evolution of the luffa AP2/ERF family, while also providing valuable insights for future studies on AP2/ERF functions. Full article

Fungal HacA/Hac1 transcription factors play a crucial role in regulating the unfolded protein response (UPR). The UPR helps cells to maintain endoplasmic reticulum (ER) protein homeostasis, which is critical for growth, development, and virulence. The Aspergillus flavus hacA gene encodes a domain rich in basic and acidic amino acids (Bsc) and a basic leucine zipper (bZip) domain, and features a non-conventional intron (Nt20). In this study, CRISPR/Cas9 was utilized to dissect the Bsc-coding, bZip-coding, and Nt20 sequences to elucidate the relationship between genotype and phenotype. In the Bsc and bZip experimental sets, all observed mutations in both coding sequences were in frame, suggesting that out-of-frame mutations are lethal. The survival rate of transformants in the Nt20 experiment set was low, at approximately 7%. Mutations in the intron primarily consisted of out-of-frame insertions and deletions. In addition to the wild-type-like conidial morphology, the mutants exhibited varied colony morphologies, including sclerotial, mixed (conidial and sclerotial), and mycelial morphologies. An ER stress test using dithiothreitol revealed that the sclerotial and mycelial mutants were much more sensitive than the conidial mutants. Additionally, the mycelial mutants were unable to produce aflatoxin but still produced aspergillic acid and kojic acid. RNAi experiments targeting the region encompassing Bsc and bZip indicated that transformant survival rates generally decreased, with a small number of transformants displaying phenotypic changes. Defects in the hacA gene at the DNA and transcript levels affected the survival, growth, and development of A. flavus. Thus, this gene may serve as a promising target for future host-induced gene-silencing strategies aimed at controlling infection and reducing aflatoxin contamination in crops. Full article