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As sequencing costs decrease, short-read and long-read technologies are indispensable tools for uncovering the genetic drivers behind bacterial pathogen resistance. This study explores the differences between the use of short-read (Illumina) and long-read (Oxford Nanopore …
Read PDFField-deployable DNA metabarcoding offers a transformative approach to biodiversity research and monitoring, yet its application remains limited due to technical constraints and a lack of reference data in poorly studied ecosystems. Combining isothermal Recombinase Polymerase …
Read PDFDengue virus (DENV) poses a growing risk in Tanzania, yet its genetic diversity in mosquito populations remains poorly understood. Using Nanopore sequencing, we recovered full coding sequences from six DENV-2 positive mosquito pools collected in …
Read PDFTomato yellow leaf curl disease is a major viral disease severely affecting tomato crops in the Mediterranean region, leading to reduced crop yield and significant economic losses. The disease is caused by monopartite begomoviruses belonging …
Read PDFThe complete genome sequence of <i>Diaporthe vaccinii</i> Shear was reported using combined Oxford Nanopore and Illumina sequencing. The hybrid genome comprises 64 contigs with a total length of 60.2 Mb and a GC content of …
Read PDF<i>Actinomyces oris</i> MG-1 is a key oral commensal involved in dental plaque formation. We report its complete genome sequence, generated using Illumina and Oxford Nanopore sequencing. The genome consists of a single circular chromosome of …
Read PDF<b>Background.</b> Our recent findings indicate that the rough form of the <i>Mycobacterium abscessus</i> complex (MABC) is associated with worse clinical outcomes compared to the smooth variant. The glycopeptidolipid (GPL) locus has been considered vital for …
Read PDFThis study combines Oxford Nanopore (ONT) third-generation sequencing with targeted amino acid metabolomics to elucidate the mechanisms underlying the structural and metabolic responses of the microbial community in Golden Ear Mushroom (<i>Naematelia sinensis</i>) during <i>Trichoderma</i> …
Read PDFIdentification of genomic rearrangements by microarrays or short-read sequencing frequently lacks information about the exact architecture and breakpoints of variants due to technical limitations. Independent verification of complex structural variants (SVs) is often performed using …
Read PDFShort tandem repeats (STRs) are highly polymorphic repetitive DNA sequences extensively used in forensic science for identification of individuals. STR genotyping is usually performed by capillary electrophoresis (CE) or next-generation sequencing (NGS) in centralized laboratories. …
Read PDFThis study reports the whole-genome sequence of <i>Achromobacter</i> sp. strain PD1, isolated from a wastewater treatment bioreactor. Using Illumina and Nanopore sequencing, a complete genome of 6,994,232 bp was obtained. This genome contains genes predicted …
Read PDF<h4>Background</h4>Polygonatum kingianum, a key species in traditional Chinese medicine, is increasingly valued for its medicinal and nutritional properties. However, wild resources are declining due to over-exploitation, necessitating genomic studies for conservation.<h4>Results</h4>Flow cytometry analysis based on …
Read PDFThe assembly of telomere-to-telomere (T2T) genomes is essential for understanding genomic architecture, especially in fungal pathogens with complex karyotypes, such as <i>Colletotrichum lini</i>, causing flax anthracnose disease. This study provides optimized guidelines for the T2T …
Read PDFThe genome of the methylotrophic methanogen <i>Methanomethylovorans thermophila</i> L2FAW is not included in the Genome Taxonomy Database (GTDB) so far, even though the strain was first described in 2005. To evaluate its genomic characteristics and …
Read PDFKombucha fermentation is driven by a Symbiotic Culture of Bacteria and Yeast (SCOBY), a cellulose-rich biofilm that hosts a complex microbial consortium. While most kombucha studies focus on the liquid beverage, the SCOBY pellicle itself …
Read PDFThe increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of population-level structural variation data. However, the effect of the length of long-reads on automated variant callers …
Read PDFThis study leveraged advanced genomic sequencing technologies, including Oxford Nanopore technology long reads, Pacific Biosciences HiFi sequencing reads, BGISEQ T7 short reads, and high-throughput chromatin conformation capture technology, to demonstrate the telomere-to-telomere genome assembly and …
Read PDFAccurate identification of RNA 5-methylcytidine (m<sup>5</sup>C) at the single-nucleotide resolution remains a central challenge in nanopore direct RNA sequencing (DRS). Current global scanning and modification-aware basecalling methods enable transcriptome-wide profiling but often yield high false-positive …
Read PDFThe white rhinoceros (<i>Ceratotherium simum</i>) offers a unique model for investigating the genomic consequences of extreme demographic bottlenecks. However, the fragmented southern white rhinoceros genome assembly has limited chromosome-scale structural and evolutionary comparisons with the …
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