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Multi-Locus Sequence Typing (MLST) is a key method for allocation of Sequence Types (STs) for bacterial isolates. Traditionally, this is performed by the Sanger sequencing method, which can be highly time-consuming and laborious. In this …
Read PDFNanopore sensors offer exceptional sensitivity for detecting single molecules, making them ideal for early disease diagnostics. In this study, we present a multiplexed nanopore-based assay that combines DNA-barcoded probes with advanced computational analysis to detect …
Read PDFSequencing of the 16S ribosomal RNA (rRNA) gene is an important tool in addition to conventional methods for the identification of bacterial pathogens in human infections. In polymicrobial samples, Sanger sequencing can produce uninterpretable chromatograms. …
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Read PDFMealybugs are aggressive pests worldwide, but few complete mitochondrial genomes have been reported. Here, we got the complete mitochondrial genome of the cotton mealybug, <i>Phenacoccus solenopsis</i> Tinsley, using Oxford Nanopore Technology. It is 14743 bp …
Read PDFThe complete genome sequence of <i>Kluyveromyces marxianus</i> strain MCHA was obtained using Illumina and Oxford Nanopore sequencing technologies. The genome comprises nine scaffolds, corresponding to the eight nuclear chromosomes and the mitochondrial genome.
Read PDF<i>Stenotrophomonas maltophilia</i> ESTM1D_MKCAZ16_6a (Sm18) is a multidrug-resistant strain isolated from river sediments in Morelos, Mexico. It is capable of replicating within acid Rab7A-positive <i>Acanthamoeba castellanii</i> phagosomes. The complete genome was assembled from Oxford Nanopore and …
Read PDF<i>Mycoplasma genitalium</i> is a fastidious human pathogen with increasing antimicrobial resistance, yet its genomic landscape remains poorly characterized due to difficulties with culture, including prolonged incubation periods and low DNA yields from both clinical and …
Read PDFSevere Fever with Thrombocytopenia Syndrome (SFTS) is caused by the SFTS virus (SFTSV) and is associated with a high mortality rate. Although previous studies have reported RNA modifications such as m6A on SFTSV RNA, an …
Read PDF<h4>Objective</h4>Premature ovarian insufficiency (POI) with short stature and mild intellectual disability can have diverse genetic etiologies. We aimed to decipher the genetic basis of this complex phenotype in a 26-year-old female with a karyotype lacking …
Read PDFSchistosomes are parasitic trematode worms of the genus Schistosoma, responsible for causing urogenital and intestinal schistosomiasis. Six primary species infect humans: S. mansoni, S. japonicum, S. mekongi, S. intercalatum, S. guineensis, and S. haematobium. In …
Read PDF<h4>Background</h4>Traditional molecular epidemiological analysis has been limited in its ability to evaluate pathogen homology, making detailed transmission pathway estimation in outbreaks challenging. Bayesian reconstruction methods using whole-genome sequencing and epidemiological data enable estimation of temporal …
Read PDFThe co-circulation of the recently emerged H5N1 clade 2.3.4.4b and the endemic H9N2 avian influenza viruses (AIV) in poultry farms has led to significant economic losses and increased the likelihood of viral reassortment. Continuous and …
Read PDFIndividual CpG methylation signatures characterize each mammalian cell type, thereby offering a powerful readout for clinical and diagnostic applications. Here, we apply this principle to in vitro cellular systems, using cell-free DNA released into the …
Read PDFHere, we report the draft genome sequences of <i>Trichoderma deliquescens</i> and <i>Aureobasidium</i> sp., fungi isolated from sediments of the Elizabeth River. Genomes assembled from Nanopore sequencing revealed genes encoding enzymes implicated in polycyclic aromatic hydrocarbon …
Read PDFRhodiola yunnanensis (Crassulaceae) is an endemic medicinal plant species distributed in the Hengduan Mountains of southwestern China. Here, we present a high-quality and near telomere-to-telomere chromosome-level genome assembly of R. yunnanensis generated using Oxford Nanopore …
Read PDFThe Icacinales order includes numerous genera and species, many of which have medicinal properties. Iodes seguinii, a species from this order, is traditionally used for treating rheumatic and inflammatory diseases. This study presents the first …
Read PDFUtricularia aurea Lour. is an aquatic herbaceous plant with yellow flowers and a unique insect-trapping mechanism, distributed in several regions of China and other Asian countries. In this study, we assembled a chromosome-scale genome of …
Read PDF<h4>Background</h4>Nanopore sequencing produces ionic current signals that are sensitive to chemical modifications in DNA and RNA molecules. However, accurate modification detection remains challenging due to limited labeled data and variability across experimental conditions.<h4>Methods</h4>We present a …
Read PDFLong-read sequencing, whether using PacBio (PB) or Oxford Nanopore Technologies (ONT), requires high-molecular-weight (HMW) DNA at high purity and free of contaminants. Here, we present a protocol for high-throughput processing of fecal samples for long-read …
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