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Highbush blueberry (Vaccinium corymbosum L.) fields can remain productive for decades. However, some older fields decline in plant health and exhibit lower yields. After re-planting with new stock, the yields continue to suffer. This condition …
Read PDFGrapevine (<i>Vitis vinifera</i> L.) cultivation is an important agricultural sector worldwide. Its expansion into new areas, like Kazakhstan, brings significant phytosanitary risks. Viroids, such as grapevine yellow speckle viroid 1 (GYSVd-1) and hop stunt viroid …
Read PDFLong intergenic non-coding RNAs (lincRNAs) are regulatory transcripts from intergenic regions with diverse expression patterns, but whether the activation of lincRNA is widespread and predictable remains unclear. Here, we applied Oxford Nanopore Technology Direct RNA …
Read PDFMetagenomics enables direct investigation of the gene content and potential functions of gut bacteria without isolation and culture. However, metagenome-assembled genomes are often incomplete and have low contiguity due to challenges in assembling repeated genomic …
Read PDF<i>Campylobacter hepaticus</i> is known to cause spotty liver disease (SLD) in layer chickens around peak production. Here, we report the complete genome sequences of two <i>C. hepaticus</i> strains, USA1 and USA5, from the United States. …
Read PDFThis research aims to assess whether sequencing the full length of the 16S rRNA gene using PacBio HiFi sequencing and Oxford Nanopore Technology (ONT) platforms outperform Illumina MiSeq platform in providing detailed specie level insights. …
Read PDF<h4>Background</h4>Intrachromosomal insertion is a rare form of structural chromosomal rearrangement that often cannot be accurately delineated by conventional G-banding, making it difficult to predict reproductive outcomes. In clinical practice, such insertions are often misinterpreted as …
Read PDF<h4>Introduction</h4>Alternative splicing (AS) is a major source of transcriptome diversity in plants, but short-read RNA sequencing (RNA-seq) has limited power for resolving full-length transcripts and complex AS patterns, particularly in perennial crops.<h4>Methods</h4>We integrated Oxford Nanopore …
Read PDFWe report genome sequences of two polar <i>Carnobacterium maltaromaticum</i> strains: 2857 (draft, 3.54 Mb, 34.4% GC) and 2862 (complete, 3.61 Mb, 34.6% GC, five plasmids). Sequencing used Illumina (both) and Nanopore (2862). Genome analysis revealed …
Read PDF<h4>Background</h4>Genetic testing is essential for disease screening, diagnosis, prognosis, and pharmacotherapy guidance. Oxford Nanopore Technologies (ONT) offers a cost-effective platform for long-read sequencing, yet its routine use in clinical diagnostics remains under evaluation. We tested …
Read PDFThe study of the application of plant growth-promoting (PGP) bacteria has increased due to their potential to enhance crop yield, improve nutrient acquisition, and increase plant tolerance to biotic and abiotic stresses. Developing synthetic microbial …
Read PDFWe report the 5.7 Mbp draft genome of carbapenem-resistant <i>Phytobacter ursingii</i> strain OUH-01, recovered from the feces of a patient with acute lymphoblastic leukemia. The genome comprises a chromosome (G+C content of 53.5%), three plasmids, …
Read PDFNanopore direct RNA sequencing (DRS) relies on adapter ligation to poly(A) tails, posing challenges for bacterial mRNAs, which naturally lack these structures. Here, we present a protocol for generating native and unmodified bacterial RNA for …
Read PDFBACKGROUND: Post-weaning diarrhoea (PWD) remains a major cause of morbidity in pig production and is commonly associated with enterotoxigenic Escherichia coli (ETEC). Conventional diagnostics rely on culturing and targeted qPCR, which provide limited resolution of …
Read PDF<h4>Introduction</h4>Recently, de novo transcriptome assembly methods have been developed to utilise long-read data in cases where a reference genome is unavailable, such as in non-model organisms. Despite the potential of these tools, there remains a …
Read PDF<b>Background.</b> Nanopore-based sequencing by Oxford Nanopore Technologies (ONT) offers rapid, cost-effective and portable sequencing. As an emerging technology, ONT must be evaluated for efficacy and practical application in both high- and low-resource settings. This scoping …
Read PDFLong-read whole-transcriptome sequencing (WTS) has the potential to precisely characterize fusion oncogenes that drive leukemia and other cancers. Although there is a variety of general-purpose fusion detection algorithms that use modern long-read sequencing data, they …
Read PDF<b>Background:</b> Despite the huge burden of deaths associated with or attributable to antimicrobial resistance, studies on sequencing based antimicrobial resistance (AMR) monitoring in Africa are scarce, specifically in the animal sector. Objective and Methods: With …
Read PDFRNA modifications add a dynamic and versatile regulatory layer to gene expression, influencing RNA stability, splicing, translation, and cellular responses. Despite their importance, traditional detection methods-such as antibody-based enrichment, chemical labeling, or indirect sequencing approaches-often …
Read PDFThe Japanese cutlassfish (Trichiurus japonicus) is a commercially important marine species across Asia. Here, we present a high-quality, chromosome-level genome assembly generated using PacBio HiFi, Hi-C, and Nanopore ONT reads. The nuclear genome comprised 24 …
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