Search Results (4,047)

The genus Quercus is an ecological keystone and economically vital component of Northern Hemisphere forests. While genomic studies have advanced our understanding of its nuclear and chloroplast genomes, the mitochondrial genomes of oaks remain less explored due to their complex evolutionary dynamics, which include extreme size variation, frequent rearrangements, and recurrent horizontal gene transfer. This study presents the assembly, annotation, and comparative analysis of mitogenomes from three closely related Asian oaks—Q. engleriana, Q. kongshanensis, and Q. tungmaiensis—using PacBio HiFi sequencing. The assemblies revealed distinct structural organizations: the Q. engleriana and Q. kongshanensis mitogenomes each comprised one circular contig and one linear contig, whereas the Q. tungmaiensis mitogenome comprised one circular contig and two linear contigs. Comparative analyses revealed variations in codon usage bias, simple sequence repeats, and predicted RNA editing sites. Notably, RNA editing in rps12 was uniquely observed in Q. kongshanensis. Mitochondrial targeting of plastid transcripts constituted 1.39%, 1.79%, and 2.24% of the mitogenomes, respectively. Phylogenetic reconstruction based on mitochondrial PCGs robustly resolved Q. kongshanensis and Q. tungmaiensis as sister species, with all three forming a distinct clade separate from other Quercus species. This study provides comprehensive mitogenomic resources essential for elucidating Quercus evolutionary biology and supporting germplasm development. Full article

Fertility is key for calf production. Direct selection for female fertility under field conditions is hindered by low accuracy and selection response. An alternative widely implemented is selection for scrotal circumference (SC), genetically correlated with daughter fertility. This study performed a genome-wide association study (GWAS) to identify genomic regions and candidate loci linked to SC and female fertility in Retinta cattle. A multivariate ssGBLUP was applied using SC records from 1061 bulls, fertility-related traits from 59,254 females and genotypes from 1230 animals using the Axiom™ Bovine Genotyping v3 Array (65k). The ssGWAS revealed 23 1-Mb windows explaining >1% of additive genetic variance for SC, one on chromosome 2 and 22 on chromosome 3. Within these windows, 198 regions spanning 118 protein-coding genes and 80 RNA genes were identified. Several genes, including GSTM3, SPATA1, HFM1, and MSH4, were previously associated with male fertility. Six regions overlapped across male and female traits, containing two protein-coding genes (THSD7B and ENSBTAG00000021755). Identification of genomic markers linked to both female fertility and male SC enables selection of superior animals, improving reproductive efficiency and advancing knowledge of the genomic basis of male–female fertility relationships. Full article

Vitamin B6 is an essential coenzyme involved in various metabolic processes critical for plant growth and development. However, its biosynthesis and regulatory mechanisms remain poorly understood in the ancient gymnosperm Ginkgo biloba. In this study, we identified two members of the PDX2 gene family (Gb_34755 and Gb_34990) through genome-wide analysis and characterized their molecular and functional properties. Bioinformatic analysis revealed distinct physicochemical traits and subcellular localizations, with Gb_34755 predicted in the cytoplasm and Gb_34990 in both chloroplasts and cytoplasm. Both proteins contain the glutaminase-related PLN02832 domain, indicating involvement in VB6 biosynthesis. Chromosomal mapping placed the genes in transcriptionally active regions on chromosomes 6 and 9. Phylogenetic analysis showed close evolutionary relationships between Ginkgo PDX2 genes and those in ferns and gymnosperms, distinct from angiosperms. Promoter analysis revealed differential enrichment of cis-elements: Gb_34990 harbored low-temperature and salicylic acid-responsive elements, while Gb_34755 showed motifs related to development. Gene expression profiling indicated significant upregulation (p < 0.05) of both genes during the late developmental stages of Ginkgo kernels, coinciding with peak VB6 content. Functional validation via transient overexpression in Nicotiana benthamiana confirmed a positive regulatory role, with VB6 levels increasing from 3.38 μg/g to 12.17 μg/g (p < 0.05). This study provides the first comprehensive functional analysis of the PDX2 gene family in Ginkgo and confirms their critical role in VB6 biosynthesis. These findings enhance our understanding of vitamin metabolism in gymnosperms and present promising targets for metabolic engineering in plants. Full article

Background/Objectives: Miscanthus Andersson, a genus of perennial grasses that includes wild relatives of key crop species, remains poorly characterized in terms of genetic diversity and evolutionary relationships. The aim of this study was to elucidate the phylogenetic structure of Miscanthus through comparative genomic analysis of the chloroplast genomes of six Korean species. Methods: Complete chloroplast genomes were assembled and analyzed for six Miscanthus species. Informative nucleotide motifs and their associated gene locations were identified as potential markers, and their phylogenetic relationships with related crops were examined. Results: The chloroplast genomes exhibited a conserved quadripartite structure, with genome sizes and GC contents within typical ranges. Analysis of codon usage showed a preference for A/U-ending codons, consistent with patterns in other angiosperms. Simple sequence repeats and long repeats demonstrated non-random distributions, indicating their value as molecular markers for phylogenetic and population studies. Comparative analyses confirmed structural conservation across Miscanthus species, whereas variation in non-coding regions provided important phylogenetic signals. Phylogenetic reconstruction based on 21 chloroplast genomes revealed four major clades, corroborating previous findings and highlighting complex evolutionary relationships within Miscanthus, including close affinities between African and Himalayan species and the genus Saccharum L. Conclusions: This study provides complete chloroplast genomes of six Miscanthus species, contributing to enhanced understanding of the relationships within the subtribe Saccharinae. The findings support the inclusion of Miscanthus species in the Korea Crop Wild Relatives inventory and highlight their potential as a genetic resource for breeding programs aimed at enhancing crop resilience to environmental stress. Full article

The cultivated peanut (Arachis hypogaea L.) is a globally important oilseed and economic crop, but its narrow genetic base limits breeding progress. Wild Arachis species represent valuable genetic resources for enhancing the resilience of the peanut cultigen. While wild species from section Arachis are widely used in breeding programs, the detection of alien chromosomes in hybrids remains challenging due to limited molecular tools. In this study, a cost-effective and efficient system was established for generating species-specific molecular markers using low-coverage next-generation sequencing data, bypassing the need for whole-genome assembly. Utilizing the Chorus2 software, specific alien-chromosome oligo (SAO) markers were developed for four wild species, A. duranensis (accession A19), A. pusilla (A10), A. appresipilla (A33), and A. glabrata (G2 and G3). A total of 1166 primer pairs were designed, resulting in 220 SAO markers specific to A. duranensis, 77 to A. pusilla, 112 to A. appresipilla, 69 to A. glabrata G2, and 59 to A. glabrata G3, with the highest development efficiency observed in A. duranensis (55.0%). These markers span all chromosomes of the five wild accessions. Genome-wide, chromosome-specific SAO markers enable the efficient detection of introgressed alien chromosomes and provide insight into syntenic relationships among homoeologous chromosomes. These markers offer an effective tool for identifying favorable genes and facilitating targeted introgression for the genetic improvement of the cultivated peanut. Full article

Background: Intracranial aneurysm (IA) rupture is a life-threatening cerebrovascular event with a mortality rate of up to 40%, affecting approximately 500,000 people globally each year. Although environmental pollutants such as 2,2′,4,4′-tetrabromodiphenyl ether (PBDE-47) have been implicated in the pathogenesis of IA, the causal relationship and underlying mechanisms remain unclear. This study aims to systematically explore the potential causal role of PBDE-47 in the development of IA by integrating multi-omics approaches. Methods: We utilized the UK Biobank Drug Proteomics Project (UKB-PPP) genome-wide association study (GWAS) data, including 2940 plasma proteins and 1400 metabolites, along with IA genetic data from 456,348 individuals, to perform a two-sample Mendelian randomization (MR) analysis. Instrumental variables were selected based on genome-wide significance (p < 5 × 10⁻⁸) or suggestive thresholds (p < 5 × 10⁻⁵). Analytical methods included inverse variance weighting (IVW), MR-Egger, weighted median, MR-PRESSO, and Steiger filtering for sensitivity analysis. Molecular docking and 100-nanosecond molecular dynamics simulations were used to evaluate interactions between PBDE-47 and proteins. Mediation analysis assessed the roles of plasma metabolites and miRNAs, and SMR-HEIDI tests were used to verify causal relationships. Results: MR analysis identified 93 plasma proteins potentially causally associated with IA, including 53 protective factors and 40 risk factors. By integrating PBDE-47 targets, IA-related genes, and metabolite-related genes, we identified 15 hub genes. Molecular docking revealed potential binding between PBDE-47 and F2R (binding energy: −5.516 kcal/mol), and SMR-HEIDI testing supported F2R as a potential causal risk factor for IA. Molecular dynamics simulations indicated the stability of the complex structure. Mediation analysis suggested that F2R may influence IA risk through eight plasma metabolites, and miR-130b-3p may indirectly promote IA development by upregulating F2R. Conclusions: Our findings suggest that exposure to PBDE-47 may have a potential causal relationship with IA risk, potentially mediated through the “PBDE–47–F2R–metabolite–miRNA” regulatory axis. These results provide preliminary evidence for early diagnostic biomarkers and targeted interventions for IA. The multi-omics analytical framework established in this study offers new insights into environmental determinants of neurovascular diseases, although further validation is needed to address potential limitations. Full article

The investigation and comparison of chloroplast genomes facilitate our deeper elucidation of the evolutionary dynamics and phylogenetics of plant species, particularly non-model plants. Opisthopappus is a genus of Asteraceae that is endemic to the Taihang Mountains in China, which includes Opisthopappus taihangensis and Opisthopappus longilobus. Although certain chloroplast genomic data are available, the comprehensive evolutionary relationships of chloroplast genomes in this genus are not yet fully understood. In this study, the assembled O. taihangensis chloroplast genomes exhibited a quadripartite structure with 131 genes, encompassing 86 protein-coding, 37 tRNA, and eight rRNA genes. The basic phylogenetic relationships of 275 Asteraceae species were consistent with preceding studies. Opisthopappus with Ajania and Chrysanthemum were gathered together in Trib. Anthemideae. However, O. taihangensis and O. longilobus were not clustered into a group. Six and eight variable hotspots were detected in Opisthopappus and Asteraceae respectively. A total of 18 optimal codons were identified in two species. Differentiation in codon usage patterns was primarily influenced by natural selection between O. taihangensis and O. longilobus. Thereinto, GCU (Ala) was specific to O. taihangensis, while ACU (Thr) was to O. longilobus. Most of the codons preferentially ended with A/U, with only two genes (rpl16 and matK) being subjected to positive selection in Opisthopappus. Under salt stress, 25 editing sites were detected in O. longilobus, and 34 editing sites were found in O. taihangensis. All editing sites were C to U transitions. Distinct editing events occurred in the two species. During the evolution of chloroplast genomes, the genes that undergo positive selection may help two Opisthopappus species to adapt the harsh cliff environment of the Taihang Mountains and ensure their normal growth and development. In response to stress, O. taihangensis and O. longilobus tended to utilize different codons and initiate unique RNA editing events. These will facilitate further work on taxonomy, phylogenetics, and adaptive evolution of Opisthopappus, even Anthemideae or Asteraceae. Full article

Autism spectrum disorder (ASD) is a complex group of severe neurodevelopmental disorders characterized by varying degrees of dysfunctional communication and social abilities as well as repetitive and compulsive stereotypic behaviors. We aim to evaluate the genetic predisposition to oxidative response and its relationship with altered oxidative stress markers in ASD patients. Genomic DNA was isolated from peripheral blood lymphocytes of 106 (83 M, 23 F; 7.9 ± 3.2 years) ASD patients and 90 healthy subjects (63 M, 27 F; 21.2 ± 1.8 years). Genotyping was performed by real-time PCR-based allelic discrimination, PCR and electrophoresis of GST deletion variants. Reactive oxygen metabolites (dROMs), the Biological Antioxidant Potential (BAP), and the advanced oxidation protein products (AOPP) were also measured. Furthermore, we assessed oxidative DNA damage by Single Cell Gel Electrophoresis. The evaluation of oxidative stress markers indicated a mild oxidative stress status and a higher level of DNA damage in nuclei of ASD patients’ lymphocytes. We found significant associations between ASD and several polymorphisms of genes involved in the detoxification and the response to oxidative stress. Genetic and environmental factors contribute to the onset of autism spectrum disorder, and ASD patients’ treatment requires a multimodal approach, including behavioral, educational, and pharmacological approaches. Full article

Genomic studies have provided key insights into the molecular pathogenesis of differentiated thyroid carcinoma (DTC), including the role of genes involved in the homologous recombination (HR) related to DNA repair and genomic stability. This research aimed to investigate the genetic landscape of HR genes in thyroid pathology, associated with recurrence risk and clinical prognosis. The study involved six individuals with thyroid conditions, including two patients diagnosed with papillary thyroid carcinoma (PTC) and four individuals with benign thyroid disease. The research material consisted of tumor samples collected during surgical procedures. Protein interactions were analyzed using the STRING database (string-db.org). Homologous recombination genes were sequenced using the HRR Panel vr1.0 on the MiSeq™ Sequencing System. Bioinformatics analysis revealed a relationship between BRAF mutations and HR gene defects in PTC. Mutations in BRCA1, BRCA2, and FANCA genes, typically associated with thyroid tumors, were identified in the tissue of papillary thyroid cancer (PTC). A statistically significant correlation was found between the FANCA gene mutation (rs7195066) and the recurrent course of the PTC. The preliminary findings suggest a potential role for non-pathogenic BARD1 mutations in follicular adenoma. No significant association was found between genes involved in homologous recombination repair and the incidence of papillary thyroid carcinoma, suggesting that these genes may not play a major role in the development of this type of thyroid cancer. Full article

Candida auris has emerged as a global public health threat due to its high mortality rates, multidrug resistance, and rapid transmission in healthcare settings. This study reports the first documented cases of C. auris candidemia in Portugal, comprising eight isolates from candidemia and colonised patients admitted to a major hospital in northern Portugal in 2023. Whole-genome sequencing (WGS) was performed to determine the phylogenetic relationships of the isolates, which were classified as belonging to Clade I. Genome sequencing also enabled the detection of missense mutations in antifungal resistance genes, which were correlated with antifungal susceptibility profiles determined according to EUCAST (European Committee on Antimicrobial Susceptibility Test) protocols and guidelines. All isolates exhibited resistance to fluconazole and amphotericin B according to the recently established EUCAST epidemiological cut-offs (ECOFFs). Most of the isolates showed a resistant phenotype to anidulafungin and micafungin. All isolates were resistant to caspofungin. Missense mutations identified included Y132F in ERG11, E709D in CDR1, A583S in TAC1b, K52N and E1464K in SNQ2, K74E in CIS2, M192I in ERG4, a novel mutation S237T in CRZ1, and variants in GCN5, a gene involved in chromatin remodelling and stress-response regulation. Identifying known and novel mutations highlights the evolution of antifungal resistance mechanisms in C. auris. These findings underscore the need for further research to understand C. auris resistance pathways and to guide effective clinical management strategies. Full article

The methylation of CpG sites with 5mC mark is a dynamic epigenetic modification. However, the relationship between the methylation and the surrounding genomic sequence context remains poorly explored. Investigation of the allele methylation provides an opportunity to decipher the interplay between differences in the primary DNA sequence and epigenetic variation. Here, we performed high-coverage long-read whole-genome direct DNA sequencing of one individual using Oxford Nanopore technology. We also used Illumina whole-genome sequencing of the parental genomes in order to identify allele-specific methylation sites with a trio-binning approach. We have compared the results of the haplotype-specific methylation detection and revealed that trio binning outperformed other approaches that do not take into account parental information. Also, we analysed the cis-regulatory effects of the genomic variations for influence on CpG methylation. To this end, we have used available Deep Learning models trained on the primary DNA sequence to score the cis-regulatory potential of the genomic loci. We evaluated the functional role of the allele-specific epigenetic changes with respect to gene expression using long-read Nanopore RNA sequencing. Our analysis revealed that the frequency of SNVs near allele-specific methylation positions is approximately four times higher compared to the biallelic methylation positions. In addition, we identified that allele-specific methylation sites are more conserved and enriched at the chromatin states corresponding to bivalent promoters and enhancers. Together, these findings suggest that significant impact on methylation can be encoded in the DNA sequence context. In order to elucidate the effect of the SNVs around sites of allele-specific methylation, we applied the Deep Learning model for detection of the cis-regulatory modules and estimated the impact that a genomic variant brings with respect to changes to the regulatory activity of a DNA loci. We revealed higher cis-regulatory impact variants near differentially methylated sites that we further coupled with transcriptomic long-read sequencing results. Our investigation also highlights technical aspects of allele methylation analysis and the impact of sequencing coverage on the accuracy of genomic phasing. In particular, increasing coverage above 30X does not lead to a significant improvement in allele-specific methylation discovery, and only the addition of trio binning information significantly improves phasing. We investigated genomic variation in a single human individual and coupled computational discovery of cis-regulatory modules with allele-specific methylation (ASM) profiling. In this proof-of-concept analysis, we observed that SNPs located near methylated CpG sites on the same haplotype were enriched for sequence features suggestive of high-impact regulatory potential. This finding—derived from one deeply sequenced genome—illustrates how phased genetic and epigenetic data analyses can jointly put forward a hypotheses about the involvement of regulatory protein machinery in shaping allele-specific epigenetic states. Our investigation provides a methodological framework and candidate loci for future studies of genomic imprinting and cis-mediated epigenetic regulation in humans. Full article

This study investigated the phylogenetic relationships in the pear calcium-dependent protein kinase (CDPK) pan-gene family and elucidated its role in the resistance to scab disease caused by Venturia nashicola. By integrating data from eight genomic sets from five cultivated pear species, Pyrus bretschneideri, P. ussuriensis, P. sinkiangensis, P pyrifolia, and P. communis, along with P. betulifolia and interspecific hybrids, 63 PyCDPK family members were identified. Among these, P. communis possessed the highest number of CDPK genes, whereas P. bretschneiderilia had the fewest. These genes encode proteins ranging from 459 to 810 amino acids in length, and are predominantly localized to the cell membrane. Six genes, PyCDPK9, PyCDPK11, PyCDPK12, PyCDPK14, PyCDPK16, and PyCDPK19, were classified as core members of the pan-genome, and PyCDPK19 showed evidence of positive selection pressure. Clustering analysis and transcriptomic expression profiling of disease-resistance-related CDPKs identified PyCDPK19 as a key candidate associated with scab resistance. Promoter analysis revealed that the regulatory region of PyCDPK19 contains multiple cis-acting elements involved in defense responses and methyl jasmonate signaling. Transient overexpression of PyCDPK19 in tobacco leaves induced hypersensitive cell necrosis, accompanied by significant increases in hydrogen peroxide (H₂O₂) accumulation and malondialdehyde (MDA) content. Similarly, overexpression in pear fruit callus tissue followed by pathogen inoculation resulted in elevated levels of both H₂O₂ and MDA. Collectively, these findings indicate that PyCDPK19 mediates defense responses through the activation of the reactive oxygen species pathway in both tobacco and pear plants, providing a promising genetic target for enhancing scab resistance in pears. Full article

Viral diseases pose a significant threat to lily (Lilium spp.) cultivation; however, large-scale assessments of virus prevalence and diversity in South Korea are limited. This study combined RT-PCR surveys, high-throughput sequencing (HTS), and analyses of 48 lily hybrid transcriptomes to characterize the lily virome. RT-PCR screening of 100 samples from 13 regions showed that 87% were infected, primarily with lily mottle virus (LMoV, 65%), Plantago asiatica mosaic virus (PlAMV, 34%), cucumber mosaic virus (CMV, 34%), and lily symptomless virus (LSV, 25%). Mixed infections were approximately twice as frequent as single infections and were associated with greater symptom severity, particularly in triple-virus combinations. High-throughput sequencing expanded detection to six viruses, including milk vetch dwarf virus (MDV) and lily virus B (LVB), the latter confirmed as a variant of strawberry latent ringspot virus (SLRSV). Near-complete genomes of several viruses were assembled and validated through RT-PCR. Transcriptome mining identified eight virus species across 26 cultivars; PlAMV was the most common, and viral loads varied significantly among hybrids. Phylogenetic analyses revealed close relationships between Korean and Chinese isolates and host-related clustering in PlAMV. These findings highlight the complexity of lily viromes in South Korea and provide essential resources for diagnostics, disease management, and biosecurity. Full article

TCP transcription factors represent a crucial family of plant regulators that contribute significantly to growth and developmental processes. Although the TCP gene family has been extensively studied in various plant species, research on Chimonanthus praecox (wintersweet) remains limited. Here, we performed genome-wide identification and analysis of the TCP gene family in C. praecox and identified 22 CpTCP genes. We further systematically examined the associated physicochemical properties, evolutionary relationships, gene structures, and regulatory features. Analysis revealed that all CpTCP proteins possess a conserved TCP domain, and subcellular localization prediction indicated their localization in the nucleus. Promoter analysis revealed that multiple cis-elements are associated with abiotic stress responses and plant growth regulation. Further analysis revealed high CpTCP2 expression in the leaves and stamen, with significantly increased levels during flower senescence. CpTCP2 expression was upregulated in response to methyl jasmonate (MeJA), salicylic acid, abscisic acid, and shade. CpTCP2 overexpression in Arabidopsis thaliana resulted in a reduced leaf area, delayed flowering, and increased rosette leaf numbers. Moreover, MeJA treatment accelerated leaf senescence in CpTCP2 transgenic Arabidopsis. These findings provide insights into the evolutionary characteristics of the TCP family in C. praecox, highlighting the functional role of CpTCP2 in regulating leaf development and flowering time in Arabidopsis, thereby offering valuable genetic resources for wintersweet molecular breeding. Full article

Paulownia trees are grown globally for their robust timber, agroforestry, and effective carbon dioxide drawdown. China possesses rich Paulownia germplasm resources, offering favorable material for the genetic improvement. Understanding the taxonomy and phylogenetic relationships of Paulownia species is essential for the advancement of germplasm innovation. In this study, we re-sequenced 67 typical accessions of 11 species within the Paulownia genus. A total of 16,163,790 high-quality single nucleotide polymorphisms (SNPs) were identified. Based on these markers, these accessions were classified into three groups: P. fortunei and P. lampropylla (Group I); P. tomentosa, P. fargesii, and P. kawakamii (Group II); and P. taiwaniana, P. jianshiensis, P. catalpifolia, P. elongata, P. ichangensis, and P. albiphloea (Group III). Using maximum likelihood estimation, population genetic structure analysis revealed that the 11 species originated from four different ancestral populations. The two predominant breeding species—P. fortunei and P. tomentosa—exhibit divergent origins: P. fortunei arose from hybridization between two ancestral species followed by complex admixture, whereas P. tomentosa retains a predominantly singular ancestral lineage, with traces of P. kawakamii. The genetic diversity (π) of P. tomentosa was 0.002588, which was considerably lower than that of P. fortunei (0.004181) suggesting that P. tomentosa is subjected to a stronger breeding selection during the evolution than P. fortunei. A total of 59 selected regions and 65 genes were identified by selective sweep analysis. These genes may be involved in biological processes such as morphological development and response to abiotic stress and hormonal activity regulation. These findings provide valuable references for further research on the genetic differentiation and adaptive evolutionary mechanisms of Paulownia species, laying a foundation for future germplasm innovation and variety improvement. Full article