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Piptanthus nepalensis (Hook.) Sweet is a leguminous shrub native to the Himalayan region and is valued for its medicinal uses and ornamental yellow flowers. Here, we report a chromosome-scale genome assembly of P. nepalensis generated …
Read PDFThe Blue-crowned Laughingthrush (Pterorhinus courtoisi) is a critically endangered species and listed as National First-class Protected Wildlife in China, with a small population size and highly restricted geographic distribution in Jiangxi Province. However, the genetic …
Read PDFCabernet Sauvignon (CS), a cultivar of winegrape (Vitis vinifera), is among the most renowned winegrape varieties globally. In this study, we released the haplotype-resolved telomere-to-telomere (T2T) CS genome assembled using a combination of PacBio HiFi, …
Read PDF<i>Flavobacterium</i> sp. strain PL002 is a psychrotolerant marine bacterium isolated from Antarctic <i>Porphyra</i> algae. This article reports the complete genome dataset of strain PL002 generated using long-read sequencing technology to improve a previously published Illumina-based …
Read PDFSaussurea hypsipeta Diels, a perennial medicinal plant used in traditional Chinese medicine, is primarily distributed on the Qinghai-Tibet Plateau, where it serves as a key component of the alpine ecosystem. The lack of genetic information …
Read PDFWith the current speed of sequencing, there is a desire for standardized and automated genome assembly and annotation to produce high-quality genomes as input for comparative (pan)genomics. Therefore, we created a convenience pipeline using existing …
Read PDF<i>Quercus oxyphylla</i> (E. H. Wilson) Hand.-Mazz. is a threatened evergreen subalpine tree species with fragmented habitats native to China. Here, we present a de novo chromosome-level genome assembly of this oak species by integrating PacBio …
Read PDFRhinogobio ventralis, a critically endangered freshwater fish endemic to the upper Yangtze River, holds significant ecological and economic value. Here, we present a high-quality chromosome-level genome assembly of R. ventralis. Using a combination of PacBio …
Read PDFChrysaora achlyos is a distinctive scyphozoan species characterized by its dark pigmentation and large size. In this study, we generated a haplotype-resolved, chromosome-scale genome assembly for C.achlyos using PacBio HiFi long reads and Hi-C technology. …
Read PDF<h4>Summary</h4>We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is …
Read PDF<h4>Background</h4>Recent outbreaks of zoonotic diseases like Ebola, Mpox, dengue fever, and COVID-19 highlight gaps in surveillance and early detection at disease hotspots. Virus family-wide diagnostic assays offer a cost-effective and sensitive alternative to metagenomics for …
Read PDF<h4>Introduction</h4>Detection of pathogens associated with bovine respiratory disease (BRD) typically involves several laboratory tools, with results limited to a defined list of targets. This study adapted a previously reported method for metagenomic sequencing of nasal …
Read PDFShotgun metagenomics enables taxonomic analysis of microbial communities by aligning sequencing reads to reference genomes, for which interpretation of alignment results often lacks standardization and relies on arbitrary abundance thresholds. This can bias species detection, …
Read PDFBACKGROUND: Shotgun metagenomics enables to study microbial communities without biases from culturing and isolation, but taxonomic classification to the species level remains challenging due to high false positive rates. Oxford Nanopore Technologies offers new opportunities …
Read PDFMetagenomic next-generation sequencing (mNGS) is increasingly employed for the diagnosis of lower respiratory tract infections (LRTIs). However, the relative diagnostic performance of long-read versus short-read sequencing platforms remains incompletely defined. For this systematic review, a …
Read PDFThe mealworm (<i>Tenebrio molitor</i>) is one of the most commonly mass-reared insects for food and feed. Monitoring the health status of commercially reared mealworm populations is of great importance for the early detection of entomopathogens …
Read PDF<h4>Introduction</h4>Very few studies have examined the diagnostic sensitivity and specificity of currently available laboratory tests for detecting respiratory pathogens in cattle, and even fewer have examined test performance on samples from animals before the onset …
Read PDFWe report the genome sequence of a human monkeypox virus isolated from an early Central European case. The 197,993 bp genome was assembled from amplicons sequenced using the Oxford Nanopore method. It has a GC …
Read PDFThe Western honeybee (Apis mellifera) is a crucial contributor to worldwide agriculture and ecological health but is experiencing wide population declines linked to Varroa mite infection. Formic Acid (FA) has been increasingly used to control …
Read PDF<h4>Main conclusion</h4>A haplotype-resolved, chromosome-scale AAC Mountainview sainfoin genome sequence along with organelle assemblies, methylome, and comparative tissue/stress-specific transcriptomes provide a solid foundation to support downstream sainfoin breeding efforts. Sainfoin (Onobrychis viciifolia Scop.) is an outcrossing, …
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