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MOTIVATION: Facioscapulohumeral Muscular Dystrophy (FSHD) is an autosomal dominant form of muscular dystrophy caused by genetic or epigenetic changes within the D4Z4-repeat at the DUX4-gene, on chromosome 4q. Genetic analysis is challenging due to a …
Read PDFVine mealybugs (<i>Planococcus ficus</i>) are an important vineyard pest. This resource announcement describes the genome sequences of three bacterial isolates from vine mealybugs that show chitinolytic activity, a trait associated with biological control potential. These …
Read PDFBACKGROUND: Direct whole genome sequencing of Capripox virus genomes from diagnostic samples is not always straightforward. Low viral content in a sample, biased sequencing and subsequent assembly and mapping methods may all influence the outcome. …
Read PDFPaenibacillus sp. TAB_01, an isolate recovered from cotton tissue culture plates and a potential novel species within the genus Paenibacillus was sequenced using Oxford Nanopore technology. The genome was 7.46 Mb with a G + …
Read PDFAdvances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality …
Read PDFZoysia macrostachya Franch. & Sav. is a halophytic perennial turfgrass in the Poaceae family, commonly found in the coastal regions of Korea, Japan, and East Asia. Z. macrostachya thrives in high-salinity environments, making it an …
Read PDFThe longhorn beetle Arhopalus rusticus (Coleoptera: Cerambycidae) is a widely distributed wood-boring pest of conifers. Here, we assembled a chromosome-level genome of A. rusticus using Illumina, Oxford Nanopore, and Hi-C sequencing technologies. The assembled genome …
Read PDFBalancing replication fork progression and origin usage is essential to maintain genome stability, but measuring replication fork progression rates and origin usage throughout the genome has been challenging. Here, we use nanopore sequencing combined with …
Read PDFRNA polymerase III (Pol III) transcribes cytosolic transfer RNAs (tRNAs) and other non-coding RNAs (ncRNAs) essential to cellular function. However, many aspects of Pol III transcription and processing, including RNA modifications, remain poorly understood, mainly …
Read PDF<h4>Introduction</h4>Accessing samples from mediastinal and hilar lymph nodes is considerably more difficult, rendering the diagnosis of tuberculous mediastinal and hilar lymphadenopathy particularly challenging. Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive interventional technique …
Read PDF<h4>Background</h4>The vaginal microbiome plays an important role in female health; it is associated with reproductive success, susceptibility to sexually transmitted infections, and, importantly, the most prevalent vaginal condition in reproduction-age women, bacterial vaginosis (BV). Traditionally, …
Read PDFBACKGROUND: The integration of human papillomavirus (HPV) DNA into the host genome is a key step in the development of HPV-associated cervical cancer (CC). However, the genomic characteristics of host genomic variations and HPV integration …
Read PDFCetaceans, despite their ability to cross wide distances, enabling mostly high levels of gene flow, can develop unique genetic lineages driven by variations in life-history traits, diverse migratory routes and local adaptation, complicating taxonomy and …
Read PDFThe global spread of SARS-CoV-2 was significantly impacted by the emergence of Variants of Concern (VOC), with Pakistan experiencing similar trends to other countries. To gain a comprehensive understanding of the genomic epidemiology of SARS-CoV-2 …
Read PDF2'-O-methylation (Nm) is pivotal in rRNA and the internal site of mRNA. Here, we present an integrated bioinformatics protocol for the identification of 2'-O-methylation using nanopore direct RNA sequencing (RNA-seq) data. We describe steps for …
Read PDFWe report complete circular genomes of five <i>Janthinobacterium lividum</i> strains isolated from Austrian freshwater sources. Genomes (6.3-6.6 Mbp, >99% complete) were assembled using Oxford Nanopore sequencing. Each encodes a full violacein biosynthesis pathway. Phylogenomic analysis …
Read PDFAlaska has the highest incidence of tuberculosis (TB) in the United States, with 8% mortality while undergoing TB treatment. With a quarter of TB cases lacking sputum culture to enable drug resistance testing, FreezeTB aimed …
Read PDFN6-methyladenosine (m6A) is the most prevalent internal mRNA modification and is enriched in the central nervous system (CNS), yet its role in glioma remains incompletely defined. Using long-read direct RNA sequencing, we mapped transcriptome-wide m6A …
Read PDFThe Korean cattle breed, Hanwoo, has been selected as a meat cattle breed since the late 1980s in Korea, but has suffered from reduced genetic diversity due to repeated selection within a single population. In …
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