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A reference genome sequence for the exceptionally long-lived Great Basin bristlecone pine, Pinus longaeva
Great Basin bristlecone pine (Pinus longaeva), one of two species of bristlecone pine, the other being Rocky Mountain bristlecone pine (P. aristata), is endemic to the high Great Basin mountains in eastern California, Nevada, and …
Read PDFThe tiger who came to T2T: Telomere-to-Telomere genome assembly of the Sumatran tiger (Panthera tigris sumatrae) using nanopore simplex reads
BACKGROUND: Chromosome-level de novo genome assemblies are vital for many aspects of biological research. Despite technological progress, achieving telomere-to-telomere assemblies remains challenging. Long-read data are critical for a contiguous genome assembly, since repeat regions cannot …
Read PDFDraft genome sequences of two <i>Ralstonia mannitolilytica</i> strains (H3G44 and H3G46) isolated from the gut of captured <i>Tenualosa ilisha</i>
We report draft genome sequences of <i>Ralstonia mannitolilytica</i> strains H3G44 and H3G46 isolated from the gut of captured <i>Tenualosa ilisha</i> in Bangladesh. Oxford Nanopore sequencing generated 4.76 and 4.77 Mb assemblies (66% GC) in three …
Read PDFFirst whole-genome assembly of the Galápagos Petrel (Pterodroma phaeopygia) using Oxford Nanopore sequencing to advance conservation genomics in a critically endangered seabird
The Galápagos Petrel (Pterodroma phaeopygia) is a critically endangered procellariiform seabird endemic to the Galápagos Islands. Once abundant, its populations have sharply declined due to invasive predators, habitat degradation, and destruction of nest burrows. Although …
Read PDFDataset of prokaryotic and eukaryotic community structures from sediment and surface water eDNA of a sustainable mangrove fisheries (SMF) aquaculture pond
Sustainable mangrove fisheries (SMF) is an integrated mangrove fisheries approach used in coastal aquaculture ponds that brings sustainability to coastal aquaculture practices. To track the positive value of mangrove on the aquaculture practices, sediment and …
Read PDFOxford nanopore technology R10 improved assembly metrics of Borrelia plasmids compared to R9
In this project, we compared whole-genome Borrelia assemblies using reads produced by Oxford Nanopore Technology (ONT) with R9 and R10 chemistry and flow cells to investigate potential improvements between versions. For this, we sequenced two …
Read PDFDraft genome sequences of <i>Streptomyces</i> strains from the H62 and H72 from the Atacama Desert, Chile
We report draft genome sequences of two <i>Streptomyces</i> strains isolated from Atacama Desert soil in Chile. Strains H62 and H72 have genome sizes of 7.9 and 8.0 Mbp with GC contents of 72.4% and 72.3%, …
Read PDFDe novo whole genome assembly of the globally invasive green shore crab Carcinus maenas (Linnaeus, 1758) via long-read Oxford Nanopore MinION sequencing
Invasive species are reshaping aquatic ecosystems worldwide at an accelerating pace, with profound ecological and economic impacts. Many crustacean species have demonstrated invasive potential or are already well-established invaders. The green shore crab, Carcinus maenas, …
Read PDFNanopore Data-Driven Near-T2T Genome Assembly of <i>Hippophae rhamnoides</i> ssp. <i>mongolica</i> Rousi and Its Complex Annotation
Sea buckthorn (<i>Hippophae rhamnoides</i> L.) is a valuable plant whose fruits are rich in biologically active compounds. We sequenced the genome of variety Triumf of <i>H. rhamnoides</i> ssp. <i>mongolica</i> Rousi on the Oxford Nanopore Technologies …
Read PDFLong-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer
<h4>Background</h4>Altered circulating cell-free DNA (cfDNA) fragmentation patterns serve as cancer biomarkers, yet standard short-read sequencing fails to capture the full fragment-length spectrum. Although cancer patients often exhibit elevated cfDNA, the relationship between high cfDNA concentration …
Read PDFResolving haplotypes of the glucose-6-phosphate dehydrogenase gene using long-range polymerase chain reaction and Oxford Nanopore sequencing
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzymopathy and poses a major concern on safe administration of oxidative drugs, including antimalarials such as primaquine and tafenoquine. Common diagnostic approaches, such as enzyme assays, …
Read PDFTranscriptome Profiling of Leaves and Roots from Rooibos (<i>Aspalathus linearis</i>) Using Oxford Nanopore Sequencing
Rooibos (<i>Aspalathus linearis</i>) is one of the few endemic South African plants that has achieved economic importance and international acclaim, mostly as a herbal tea. Plant production, limited to a small mountainous region in South …
Read PDFThe detection of three independent benzimidazole resistance mutations in a single Ancylostoma caninum population from a Golden Retriever breeding kennel in Sao Paulo, Brazil
Multiple anthelmintic drug resistance (MADR) is widespread in the canine hookworm Ancylostoma caninum in kenneled greyhounds in the USA and Australia with benzimidazole resistance being associated with the isotype-1 β-tubulin SNPs Q134H(CAA > CAT) and …
Read PDFEvaluation of Oxford Nanopore Technologies workflows for genomic epidemiology of outbreak-associated bacterial isolates in the clinical setting
Accurate and efficient whole-genome sequencing (WGS) is crucial for clinical diagnostics and surveillance of bacterial infections. Here, we investigate the potential of a new Oxford Nanopore Technologies (ONT) workflow for WGS of clinically relevant bacterial …
Read PDFTechnical feasibility of a long read, fourth generation sequencing platform in diagnostic profiling of clinical routine samples: a proof-of-concept study
<h4>Background</h4>Next generation sequencing (NGS) impacted on clinical algorithm of solid tumor patients. A heterogeneous series of NGS platforms have been implemented in clinical practice but challenging handling procedures, high technical costs, and scant affordability on …
Read PDFEffect of sialidase inhibitors on a plaque community biofilm model
The oral microbiome is a diverse ecosystem that plays a critical role in health and disease and contains numerous bacterial species capable of metabolizing host-derived glycans, particularly sialic acids. Sialidase enzymes can be produced by …
Read PDFStreptococcus canis outbreak affecting farmed mink (Neogale vison) in Northwestern Greece
The present study describes an outbreak of Streptococcus canis (S.canis) infection in a commercial mink farm in West Macedonia, Greece, and investigates its clinical, pathological and microbiological features.In late February 2024, approximately 300 out of …
Read PDFNear-complete genome sequences of equine herpesvirus (EHV) 1, EHV-3, and EHV-4 from the USA using a hybrid assembly approach
We report near-complete genome sequences of equine herpesvirus (EHV) 1, 3, and 4 from the USA. Hybrid assemblies combining Illumina and Oxford Nanopore reads yielded high-quality genomes, enhancing understanding of EHV diversity and evolution in …
Read PDFHidden Fungal DNA Structures May Shape Sequencing Outcomes
Fungal DNA is systematically under-detected in shotgun metagenomics, likely due in part to physical barriers like melanized cell walls and complex DNA conformations. Additionally, Oxford Nanopore Technologies sequencing with native fungal DNA often results in …
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