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This 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 PDFThe concept of viral quasispecies refers to a constantly mutating viral population occurring within hosts, which is essential for grasping the micro-evolutionary patterns of viruses. Despite its high error rate, long-read sequencing holds potential for …
Read PDF<h4>Background</h4>Native long-read DNA sequencing simultaneously captures genetic variants and epigenetic modifications from single molecules, but preserving molecular length and base modifications currently depends on cold-chain infrastructure that limits access to well-resourced settings.<h4>Results</h4>We demonstrate that ensilication, …
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 …
Read PDFThe methylation of CpG sites with 5mC mark is a dynamic epigenetic modification. However, the relationship between the methylation and the surrounding genomic sequence context remains poorly explored. Investigation of the allele methylation provides an …
Read PDFThe exploration of microbial genomes through next-generation sequencing (NGS) and genome mining has transformed the discovery of natural products, revealing an immense reservoir of previously untapped chemical diversity. Bacteria remain a prolific source of specialized …
Read PDFDiscovery of disease-related bacterial biomarkers could be a useful approach for early prevention or diagnosis of various afflictions, such as colorectal cancer. This typically involves analyzing small regions of the 16S rRNA gene (e.g. V3V4) …
Read PDF<h4>Key message</h4>The first genome-wide evidence of 6 mA methylation in the organellar genomes of Riccia fluitans was provided by this study, with methylation patterns being shown to differ between aquatic and terrestrial forms, suggesting that …
Read PDFFoodborne enteric infections are a major public health and economical burden, yet their surveillance often relies on latent indicators that delay containment efforts by several days and weeks. Conversely, whole metagenome shotgun sequencing of communal …
Read PDFBACKGROUND: Hemophilia A (HA) is an X-linked recessive bleeding disorder caused by pathogenic variants in the F8 gene, resulting in deficient coagulation factor VIII activity. Although intron 22 and intron 1 inversions (Inv22 and Inv1) …
Read PDF<h4>Background</h4>Ongoing antimalarial drug resistance surveillance is essential to guide effective treatment strategies. Historically, resistance to chloroquine and sulfadoxine-pyrimethamine (SP) has been associated with well-characterized mutations in the chloroquine resistance transporter (Pfcrt; K76T) and antifolate pathway …
Read PDFA fully phased, chromosome-level reference genome assembly for an IUCN-declared critically endangered and paleo-endemic tree, Eidothea hardeniana (Nightcap Oak) was assembled de novo using long-read PacBio HiFi, Oxford Nanopore (ONT) and Hi-C sequencing technologies. Consensus …
Read PDFThe draft genome of <i>Kitasatospora</i> sp. HPM-01-4 was sequenced using the ONT PromethION platform, yielding 12 scaffolds with a total genome size of 9.5 Mb, comprising a 9.1 Mb main contig and 11 shorter contigs.
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