Search Results (409)

Prader–Willi (PWS) and Angelman (AS) syndromes were the first examples in humans with errors in genomic imprinting, usually from de novo 15q11-q13 deletions of different parent origin (paternal in PWS and maternal in AS). Dozens of genes and transcripts are found in the 15q11-q13 region, and may play a role in PWS, specifically paternally expressed SNURF-SNRPN and MAGEL2 genes, while AS is due to the maternally expressed UBE3A gene. These three causative genes, including their encoding proteins, were targeted. This review article summarizes and illustrates the current understanding and cause of both PWS and AS using strategies to include the literature sources of key words and searchable web-based programs with databases for integrated gene and protein interactions, biological processes, and molecular mechanisms available for the two imprinting disorders. The SNURF-SNRPN gene is key in developing complex spliceosomal snRNP assemblies required for mRNA processing, cellular events, splicing, and binding required for detailed protein production and variation, neurodevelopment, immunodeficiency, and cell migration. The MAGEL2 gene is involved with the regulation of retrograde transport and promotion of endosomal assembly, oxytocin and reproduction, as well as circadian rhythm, transcriptional activity control, and appetite. The UBE3A gene encodes a key enzyme for the ubiquitin protein degradation system, apoptosis, tumor suppression, cell adhesion, and targeting proteins for degradation, autophagy, signaling pathways, and circadian rhythm. PWS is characterized early with infantile hypotonia, a poor suck, and failure to thrive with hypogenitalism/hypogonadism. Later, growth and other hormone deficiencies, developmental delays, and behavioral problems are noted with hyperphagia and morbid obesity, if not externally controlled. AS is characterized by seizures, lack of speech, severe learning disabilities, inappropriate laughter, and ataxia. This review captures the clinical presentation, natural history, causes with genetics, mechanisms, and description of established laboratory testing for genetic confirmation of each disorder. Three separate searchable web-based programs and databases that included information from the updated literature and other sources were used to identify and examine integrated genetic findings with predicted gene and protein interactions, molecular mechanisms and functions, biological processes, pathways, and gene-disease associations for candidate or causative genes per disorder. The natural history, review of pathophysiology, clinical presentation, genetics, and genetic-phenotypic findings were described along with computational biology, molecular mechanisms, genetic testing approaches, and status for each disorder, management and treatment options, clinical trial experiences, and future strategies. Conclusions and limitations were discussed to improve understanding, clinical care, genetics, diagnostic protocols, therapeutic agents, and genetic counseling for those with these genomic imprinting disorders. Full article

Dentathalia scutellariae (Hymenoptera: Athaliidae) is a major pest of Scutellaria baicalensis, a plant of significant economic and medicinal value. To date, no genomic resources have been available for this species, limiting research into its biology and control. Here, we reported a genome assembly of D. scutellariae with high accuracy and contiguity, sequenced by PacBio HiFi long-read and MGI-Seq short-read methods. The genome assembly is 157.00 Mb in length with a contig N50 of 4.04 Mb. The complete BUSCO score was 98.8%. The genome contained 14.73 Mb of repetitive elements, representing 9.38% of the total genome size. We predicted 14,904 protein-coding genes, of which 12,327 genes were annotated functionally. Gene family analysis of D. scutellariae revealed 422 expanded and 113 contracted gene families. Notably, genes within expanded families were significantly enriched in retinol metabolism and drug metabolism–cytochrome P450 pathways. We present the first high-quality genome assembly of D. scutellariae, which serves as a foundational genomic resource. This dataset will facilitate future studies on the molecular basis of D. scutellariae’s pest status, host adaptation, and the development of targeted control strategies. Full article

Leishmania guyanensis is one of 15 American human-pathogenic species, frequently linked to therapeutic failure due to its marked genetic plasticity and adaptability under drug pressure. To broaden the genomic understanding of this species, its biological traits, and potential therapeutic alternatives, we sequenced the L. guyanensis strain MHOM/BR/75/M4147. Raw reads underwent quality-filtering and assembly. Taxonomic classification utilized BLASTn and Kraken2, confirming that 99.95% of contigs matched Leishmania. The assembled genome size was 31 Mb, with an N50 of 4743 bp and 40.85× coverage. Variant calling subsequently identified 36,665 SNPs, 8210 indels, and chromosomal aneuploidies. Genomic annotation identified 3119 proteins with known molecular functions in L. guyanensis, alongside 6371 orthologous genes shared with L. major and L. panamensis. The search for pharmacological relevance yielded ten candidate genes, including one calpain and nine GSK3 family members. Phylogenetic reconstruction using the polA1 gene consistently grouped L. guyanensis, demonstrating strong discriminatory capacity, with L. martiniquensis emerging as the most divergent species. Overall, these findings expand the available genomic framework for L. guyanensis and support advances in species-specific diagnostic approaches. Full article

Background: Erysipelothrix rhusiopathiae is an important zoonotic pathogen in poultry, yet little is known about its antimicrobial resistance (AMR) dynamics in avian hosts. With growing concerns about subtherapeutic antimicrobial use in animal agriculture, poultry-origin isolates represent a potential but under-characterized reservoir of resistance genes. Methods: We phenotypically tested 38 E. rhusiopathiae strains isolated from geese, ducks, and turkeys in Hungary (2024) using broth microdilution against 18 antimicrobial agents, following Clinical Laboratory Standards Institute (CLSI) guidelines. Nineteen phenotypically resistant strains were selected for whole-genome sequencing (Illumina platform), followed by de novo hybrid assembly, gene annotation (Prokka, CARD, VFDB), mobile element detection (Mobile Element Finder), and phylogenetic inference (autoMLST). Results: All isolates were susceptible to β-lactams, including penicillin, amoxicillin, and third-generation cephalosporins. Resistance to tetracyclines (up to 10.5%) and florfenicol (5.3%) was most frequently detected. Genomic analysis revealed the presence of tetM (9/19), tetT (2/19), and erm(47) (2/19) genes, all associated with chromosomally integrated mobile elements, ICE Tn6009 and IS ISErh6. Phylogenomic analysis demonstrated tight clustering into four clades, suggesting clonal expansion. Notably, one strain harbored a 64.8 kb genomic island carrying ermC, the first such finding in poultry-derived E. rhusiopathiae. Conclusions: Our data highlights the early emergence of mobile AMR determinants in E. rhusiopathiae from poultry and suggests that horizontal gene transfer may drive resistance even in chromosomally encoded contexts. The genomic stability and phylogenetic homogeneity of avian isolates underscore the need for targeted AMR surveillance in poultry sectors to mitigate potential zoonotic transmission risks. Full article

The genetic improvement of Phalaenopsis-type Dendrobium, a valuable ornamental and medicinal orchid, is hindered by the lack of a complete reference genome. In this study, a transcriptome-based approach was employed to develop and validate insertion–deletion (InDel) markers for genetic analysis and variety identification. RNA-seq was performed on two distinct varieties, resulting in the de novo assembly of 156,108 unigenes. A bioinformatics pipeline was developed to identify 5083 high-quality InDel loci, from which 1029 potential markers were designed. Fifty primer pairs were selected and validated experimentally, with 84% successfully amplifying clear products, and 76% showing polymorphism. The polymorphism information content (PIC) of the markers ranged from 0.25 to 0.78, indicating their high potential for use in genetic diversity studies. These markers were used to classify 24 Phalaenopsis-type Dendrobium varieties into distinct genetic clusters. This work provides a scalable and robust platform for molecular breeding, DNA fingerprinting, and germplasm management in non-model species that lack a reference genome. By leveraging transcriptome data, these markers will contribute to the efficient genetic improvement of Dendrobium and other similar crops. Full article

Starry flounder (Platichthys stellatus) is extensively farmed in Korea, and the importance of aquaculture technology in the economic and industrial sectors continues to grow. However, pigmentation anomalies, such as skin discoloration during farming, have resulted in significant economic losses. Despite continuous research to uncover the underlying causes, genomic research in this area remains insufficient. This study utilized RNA-seq with de novo assembly analysis to establish candidate genes in brain tissue related to pigmentation variation in P. stellatus. Genes associated with albinism and melanism were identified, with 1053 genes linked to albinism and 642 genes associated with melanism. Functional analysis of these genes was also conducted using gene ontology analysis, categorizing the genes according to biological processes, cellular components, and molecular functions. KEGG pathway analysis revealed significant associations with five pathways for albinism and two pathways for melanism in brain tissue. The large-scale gene expression profiles identified in this study provide valuable genomic resources for future studies of aquaculture species, including P. stellatus. While the findings provide valuable genomic insights, the study was limited to brain tissue analysis and requires further gene-level validation. Full article

This study examines the genomic composition and resistance potential of eight putative plasmid-derived contig assemblies reconstructed from marine Enterobacterales isolated in the central Adriatic Sea. Using a combination of Illumina-based whole genome sequencing, de novo assembly, and a multi-tool bioinformatics pipeline, we annotated antimicrobial resistance genes (ARGs), insertion sequences (ISs), and plasmid replicon types. Clinically significant resistance markers such as bla_KPC, bla_TEM, aacA4, tetA, and folP were identified, frequently co-localised with mobile genetic elements including IS110, IS4, and IS1182. The plasmid-associated contigs were assigned to MOBP and MOBQ types and contained replicon markers (IncP6, IncA/C2) characteristic of broad-host-range plasmids. Our findings provide valuable insight into the plasmidome of environmental Enterobacterales, emphasising the role of coastal pollution in shaping the distribution and potential mobility of antimicrobial resistance genes. This supports the One Health framework by linking environmental reservoirs to clinically relevant resistance mechanisms. Full article

Background/Objectives: Chloroplast genomes (plastomes) are valuable for fern systematics, yet the epiphytic lineages have remained underexplored. Methods: The Davallia trichomanoides plastome was de novo assembled from Illumina data and annotated. Results: The plastome measures 154,217 bp with a GC content of 40.82% and contains 115 genes. Comparative analysis reveals two inverted repeat (IR) size classes (~24.0–24.6 kb vs. ~27.4–27.5 kb) and lineage-specific shifts at the IR junctions. For instance, the ndhF gene remains in the small single copy (SSC) region in D. trichomanoides and Drynaria acuminata, but it crosses into the IRb region in other species. We observed nucleotide diversity hotspots in the large single copy (LSC) and SSC regions. The IR regions are highly conserved. The ratios of nonsynonymous to synonymous substitutions (Ka/Ks) are mostly less than 1, indicating purifying selection. Phylogenetic analysis places D. trichomanoides as the sister to D. acuminata. Conclusions: This study highlights the stable plastome structure of D. trichomanoides and identifies candidate loci for barcoding. It also supports the stable placement of Davallia within the epiphytic Polypodiineae. Full article

Background/Objectives: The butterfish Stromateus stellatus is undervalued and usually discarded as bycatch, leading to an inefficient and unsustainable use of marine biomass. Overall, although Stromateus is the type genus of the family Stromateidae, its species are less studied than more economically important fishes. Methods: In this study, we determined and analyzed the complete mitochondrial genome sequence of S. stellatus. Furthermore, we performed maximum likelihood and Bayesian inference analyses to infer the phylogenetic relationships among 21 species of the order Scombriformes. Results: Using next-generation sequencing (NGS) and de novo assembly, a circular mitochondrial genome of 16,509 bp was obtained, exhibiting the typical vertebrate mitochondrial structure comprising 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Three intergenic regions were identified, including the control region and the origin of light-strand replication, along with several gene overlaps. The heavy strand nucleotide composition was determined to be 28.79% A, 27.84% C, 16.32% G, and 27.05% T, with a GC content of 44.16%. The three Peprilus and five Pampus species formed a clade together with S. stellatus, supported by high bootstrap and posterior probability values, confirming the monophyly of Stromateidae. Conclusions: The gene order and content are consistent with those reported for other Stromateidae species and correspond to the typical arrangement observed in most bony fishes. This mitochondrial genome represents the first one reported for the genus Stromateus, providing valuable insights into the genetic makeup of S. stellatus, contributing to a better understanding of marine biodiversity. Additionally, these data will support future research on pelagic fish evolution and assist in sustainable fisheries management. Full article

Genome sequencing has possibly been the greatest step in the development of advanced tools for animal genetic improvement: knowledge of gene sequences and use of haplotype markers for productivity traits can provide important improvements in yield production and optimisation of reproductive program. Next-generation and, more recently, third-generation sequencing techniques enormously increased the ability to produce sequences from single individuals and increased the interest in exome or whole-genome sequencing as an alternative to SNP chips in breeding programs as these techniques allowed for the capture of a wider range of variations, including characterisation of rare variants, structural variations, and copy number changes. Here, we present a procedure, based on fast de novo assembly and a scaffolding step, to quickly build an almost complete genome starting from long reads obtained in a single sequencing run. The procedure, applied to sequences from five water buffaloes, was able to independently build, for each individual, an almost complete high-quality genome with highly continuous chromosome sequences; in most cases, over 90% of the length of the reference chromosome was covered by less than ten long contigs. Unlike other pipelines based on slower assemblers or which require many sequencing data, in 1–2 days, the proposed procedure can go from a single run to continuous genome assembly, supporting fast analysis of large chromosome structures, potentially useful for improving animal breeding and productivity. Full article

Bacteriophages have been widely investigated as a promising treatment of food, medical equipment, and humans colonized by antibiotic-resistant bacteria. Phages pose particular interest in combating those bacteria which form biofilms, such as the medically important human pathogen Pseudomonas aeruginosa and several plant pathogens, including P. syringae. In an undergraduate lab course, P. putida was used as the host to isolate novel anti-pseudomonal bacteriophages. Environmental samples of soil and water were collected, and purified phage isolates were obtained. After Illumina sequencing, genomes of these phages were assembled de novo and annotated. Assembled genomes were compared with known genomes in the literature and GenBank to identify taxonomic relations and to refine their functional annotations. The thirteen phages described are sipho-, myo-, and podoviruses in several families of Caudoviricetes, spanning several novel genera, with genomes ranging from 40,000 to 96,000 bp. One phage (DDSR119) is unique and is the first reported P. putida siphovirus. The remaining 12 can be clustered into four distinct groups. Six are highly related to each other and to previously described Autotranscriptaviridae phages: Waldo5, PlaquesPlease, and Laces98 all belong to the Waldovirus genus, whereas Stalingrad, Bosely, and Stamos belong to the Troedvirus genus. Zuri was previously classified as the founding member of a new genus Zurivirus within the family Schitoviridae. Ebordelon and Holyagarpour each represent different species within Zurivirus, whereas Meara is a more distantly related member of the Schitoviridae. Dolphis and Jeremy are similar enough to form a genus but have only a few distant relatives among sequenced phages and are notable for being temperate. We identified the lysis cassettes in all 13 phages, compared tail spike structures, and found auxiliary metabolic genes in several. Studies like these, which isolate and characterize infectious virions, enable the identification of novel proteins and molecular systems and also provide the raw materials for further study, evaluation, and manipulation of phage proteins and their hosts. Full article

In recent years, symptoms of Twig Cankers and Shoot Blight (TCSB) have re-emerged in several Italian peach orchards, particularly within key production areas of the Emilia-Romagna region. The fungal pathogen Diaporthe amygdali is recognized as the primary causal agent of TCSB, leading to the rapid desiccation of shoots, flowers, leaves, and branches, often accompanied by resin exudation from cankers that appear in late winter or early spring. Given Italy’s position as the second-largest peach producer in Europe, ensuring sustainable yields and high fruit quality necessitates a deeper understanding of D. amygdali biology and the development of effective diagnostic and management tools. This study employed a hybrid whole-genome sequencing strategy, combining Illumina short-read and PacBio long-read technologies, to generate the first high-quality genome assembly of D. amygdali isolated from peach. The genome analysis revealed candidate virulence genes and other factors involved in pathogenicity, deepening our understanding of the infection strategies employed by D. amygdali. These findings may support the potential development of sustainable, effective strategies against TCSB, ultimately supporting resilient peach production in Italy and beyond. Full article

Background/Objectives: Fissidens crispulus Brid. is a dioicous moss with conspicuous axillary hyaline nodules and serrulate leaf margins. It features Neoamblyothallia-type peristome teeth and serves as an ecologically significant model for studying adaptation in the hyperdiverse genus Fissidens (>440 species). Methods: In this study, the complete chloroplast genome of F. crispulus was sequenced and de novo assembled, enabling detailed comparative genomic, phylogenetic, and codon usage bias studies. Results: As the third fully sequenced member of Fissidentaceae, this study deciphers its 124,264–124,440 bp quadripartite genome encoding 129 genes (83 CDS, 32 tRNAs, 8 rRNAs). Repeat analysis identified 125–127 SSRs, dominated by mono-/di-nucleotide A/T repeats (>70%), and dispersed repeats predominantly forward (F) and palindromic (P) (>85%), confirming profound AT-biased composition (GC content: 28.7%). We established 7 hypervariable loci (matK, ycf2, etc.) as novel Dicranidae-wide phylogenetic markers. Codon usage exhibited significant A/U-ending preference, with 12 optimal codons (e.g., GCA, UGU, UUU) determined. Maximum likelihood analyses resolved F. crispulus and F. protonematicola as sister groups with high support value (MBP = 100%). Conclusions: This work provides the foundational cpDNA resource for Fissidens, filling a major gap in bryophyte chloroplast genomics and establishing a framework for resolving the genus’s infrageneric conflicts. Furthermore, it offers critical insights into bryophyte plastome evolution and enables future codon-optimized biotechnological applications. Full article

Tall fescue toxicosis, caused by ingestion of endophyte-infected tall fescue (Lolium arundinaceum), impairs growth and reproduction in beef cattle and results in over USD 3 billion annual loss to the U.S. livestock industry. While the effects on host metabolism and rumen function have been described, the impact on the rectal microbiome remains poorly understood. In this study, we performed whole-genome shotgun metagenomic sequencing on fecal samples collected before and after a 30-day toxic fescue seed supplementation from eight pregnant Angus × Simmental cows and heifers. We generated 157 Gbp of sequencing data in 16 metagenomes, and assembled 13.1 Gbp de novo microbial contigs, identifying 22 million non-redundant microbial genes from the cattle rectum microbiome. Fescue toxicosis significantly reduced alpha diversity (p < 0.01) and altered beta diversity (PERMANOVA p < 0.01), indicating microbial dysbiosis. We discovered significant enrichment of 31 bacterial species post-treatment, including multiple core rumen taxa. Ruminococcaceae bacterium P7 showed an average of 16-fold increase in fecal abundance (p < 0.01), making it the top-featured species in linear discriminant analysis. Functional pathway analysis revealed a shift from energy metabolism to antimicrobial resistance and DNA replication following toxic seed consumption. Comparative analysis showed increased representation of core rumen taxa in rectal microbiota post-treatment, suggesting disrupted rumen function. These findings demonstrate that fescue toxicosis alters both the composition and functional landscape of the hindgut microbiota. Ruminococcaceae bacterium P7 emerges as a promising biomarker for monitoring fescue toxicosis through non-invasive fecal sampling, with potential applications in herd-level diagnostics and mitigation strategies. Full article

The pan-plastome approach provides a powerful tool for investigating intraspecific divergence and population genetics due to its unique advantages, including single-copy genes, absence of recombination, and moderate nucleotide substitution rates. Adenocaulon himalaicum Edgew. (Asteraceae), a widely distributed medicinal herb in East Asia, remains genomically understudied at the population level, with no comprehensive pan-plastome assembly available to date. Here, we de novo assembled pan-plastome of 87 individuals from 18 populations representing its known distribution range. The pan-plastome exhibited a typical quadripartite structure (152,129 bp to 152,207 bp), containing 113 unique genes, most of which were under purifying selection. Phylogenetic and haplotypes analyses revealed three distinct genetic lineages corresponding to their geographic distribution. Population genetic analyses showed significant differentiation among three genetic groups (AMOVA: 73.43% variation among groups) and a strong isolation-by-distance pattern (IBD: r = 0.469, p = 0.001). The pronounced population structure underscores the imperative for establishing distinct conservation units, with particular emphasis on marginal populations that may harbor unique genetic compositions and potential medicinal properties. Our study presents the first pan-plastome for A. himalaicum, offering new insights into its plastome evolution and population divergence, providing valuable genomic resources to guide future breeding and sustainable utilization of medicinal herbs. Full article