Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species iden...
In this study, we report on the full genome phylogenetic analysis of four ASFV isolates obtained from wild boars in Russia. These samples originated from two eastern and two western regions of Russia in 2019. Phylogenetic analysis indicated that the...
Primula comprises many species of horticultural value. In Korea, six species grow in the wild. Yamazaki classified the variety Primula modesta var. fauriei into P. modesta var. hannasanensis and P. modesta var. koreana based on the differences in lea...
Background: This research aims to enhance the genomic database of Klebsiella oxytoca by identifying virulence genes through the whole genome sequencing and comparative analysis of a goat-derived K. oxytoca (KOHN1) strain, while clarifying the relatio...
We have sequenced the chloroplast genome of red spruce (Picea rubens) for the first time using the single-end, short-reads (44 bp) Illumina sequences, assembled and functionally annotated it, and identified simple sequence repeats (SSRs). The contigs...
A comprehensive overview of the recent physics-inspired genome analysis tool, GenomeBits, is presented. This is based on traditional signal processing methods such as discrete Fourier transform (DFT). GenomeBits can be used to extract underlying geno...
Clostridium perfringens (C. perfringens) is an important veterinary pathogen and a noteworthy threat to human and animal health. Recently, there has been a significant rise in the number of moose fatalities caused by this rare, endemic species in Chi...
Kohlrabi is an important swollen-stem cabbage variety belonging to the Brassicaceae family. However, few complete chloroplast genome sequences of this genus have been reported. Here, a complete chloroplast genome with a quadripartite cycle of 153,364...
Trichosporon austroamericanum is a recently described yeast species related to Trichosporon inkin and exclusively isolated from clinical specimens. However, its genomic features and pathogenic potential remain poorly understood. In this study, we per...
The plant mitochondria play a crucial role in various cellular energy synthesis and conversion processes and are essential for plant growth. Watercress (Oenanthe javanica) is a fast-growing vegetable with strong adaptability and wide cultivation rang...
Human adenovirus species C (HAdV-C) is frequently detected in China and worldwide. For the first time, 16 HAdV-C strains were isolated from sewage water (14 strains) and hospitalised children with diarrhoea (2 strains,) in Tianjin, China. Nearly comp...
Mpox, a zoonotic disease caused by the mpox virus (MPXV), has seen a significant shift in its epidemiological status since 2022, evolving from an initial local outbreak to a global epidemic. This recent outbreak of MPXV mainly emerged in several Euro...
Background: The Tibetan chicken has adapted well to high altitudes genetically after its long-term habitation in the plateau. In this study, we analyzed the selection signal of Tibetan black chickens (TBCs) and discovered genes associated with the ch...
The growing prevalence of antibiotic-resistant Staphylococcus aureus strains mandates selective susceptibility testing and epidemiological investigations. It also draws attention to an efficient typing strategy. Whole genome sequencing helps in genet...
The availability of whole genome sequences in public databases permits genome-wide comparative studies of various bacterial species. Whole genome sequence-single nucleotide polymorphisms (WGS-SNP) analysis has been used in recent studies and allows t...
Emericellopsis species from extreme environmental conditions provide a rich source of unique and biologically active secondary metabolites. The paper exhibits a comprehensive genomic analysis including complete genome sequencing, phylogenetic reconst...
We performed whole genome sequencing and genetic characterization of rabies viruses (RABV) detected in bats submitted to the Connecticut Veterinary Medical Diagnostic Laboratory (CVMDL) during 2018–2019. Among 88 bats submitted to CVMDL, six br...
A series of human and animal diseases that are caused by Salmonella infections pose a serious threat to human health and huge economic losses to the livestock industry. We found antibiotic resistance (AR) genes in the genome of 133 strains of S. Indi...
Smith–Magenis syndrome is a complex neurobehavioral genetic disorder with a broad phenotypic spectrum. While the etiology of SMS is commonly attributed to one-copy interstitial deletion in the 17p11.2 region (90–95% of cases), variants id...
Mycobacterium abscessus is an important pathogen that can cause serious human diseases and is difficult to treat due to antibiotic resistance. In this study, we analyzed, using whole-genome sequence (WGS) data, M. abscessus strains serially isolated...
Objective: Absence of homozygosity (AOH) is a genetic characteristic known to cause human diseases mainly through autosomal recessive or imprinting mechanisms. The importance and necessity of accurate AOH detection has become more clinically signific...
As one of the commonly isolated endophytic fungi, Alternaria has been known for the production of numerous secondary metabolites (SMs). However, its detailed genomic features and SM biosynthetic potential have not been extensively studied thus far. T...
Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen of public health concern, requiring a One Health approach to clarify its transmission and distribution. However, its prevalence and genomic characteristics in livestock and companio...
A unique line of Holstein cattle has been maintained without selection in Minnesota since 1964. After many generations, unselected cattle produce less milk, but have better reproductive performance and health traits when compared with contemporary co...
The genus Ormosia comprises approximately 130 species, which are found in tropical regions all over the world. The taxonomy and evolutionary history are still ambiguous due to the lack of a solid phylogeny at the species level. Due to the fast advanc...
Burkholderia glumae is one of the most critical rice-pathogenic bacteria, and it causes bacterial panicle blight (BPB) in rice plants. In 2017, BPB symptoms were observed from rice fields in Chiang Rai, Northern Thailand. Sixty-one isolates obtained...
Bougainvillea (Nyctaginaceae) is a popular ornamental plant group primarily grown for its striking colorful bracts. However, despite its established horticultural value, limited genomic resources and molecular studies have been reported for this genu...
Ehretiaceae is a family in the order Boraginales. It contains more than 150 species. The Ehretiaceae classification has remained elusive and changed over time from subfamily to family, or vice versa. In this paper, we sequenced, characterized, and an...
Campylobacter spp. are a leading and increasing cause of gastrointestinal infections worldwide. Source attribution, which apportions human infection cases to different animal species and food reservoirs, has been instrumental in control- and evidence...
Adzuki bean (Vigna angularis) is an important pulse crop, and rust disease severely restricts its production. Identifying resistance genes is essential for accelerating the development of rust-resistant cultivars through marker-assisted breeding. In...
Whole genome sequencing (WGS) is widely used for outbreak analysis of bacteriology and virology but is scarcely used in mycology. Here, we used WGS for genotyping Aspergillus fumigatus isolates from a potential Aspergillus outbreak in an intensive ca...
Nuclear mitochondrial DNA sequences (NUMTs) are mitochondrial DNA fragments in the nuclear genome, and their unclear distribution in Chrysomelidae species hinders the selection of accurate molecular markers for species identification and phylogenetic...
Interspecific hybridization often shows negative effects on hybrids. However, only a few multicellular species, limited to a handful of plants and animals, have shown partial genetic mechanisms by which hybridization leads to low fitness in hybrids....
Cytokinins play an important role in plants and are targets of wheat breeding, particularly in terms of flowering and yield. The objective of this study was to determine relative synonymous codon usage (RSCU), molecular weight (g/mol), theoretical is...
Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking in the food industry thanks to several developments in recent years. However, the cost associated to this technology and the degree of expertise required...
The Belian (Eusideroxylon zwageri Teijsm. & Binn.) is a commercially important timber species in Southeast Asia that was listed on the IUCN Red List of threatened species in 1998. Six years ago, we published an article in Genome Biology Ecology e...
In this paper, we propose a computational strategy for performing genome-wide analyses of intergenic sequences in bacterial genomes. Following similar directions of a previous paper, where a method for genome-wide analysis of eucaryotic Intergenic se...
Astragalus L. (Fabaceae), the largest plant genus with significant medicinal value, faces critical endangerment of its wild resources and a scarcity of chloroplast genomic data. We sequenced and assembled the complete chloroplast (cp) genomes of four...
Dianthus spp. is a genus with high economic and ornamental value in the Caryophyllaceae, which include the famous fresh-cut carnation and the traditional Chinese herbal medicine, D. superbus. Despite the Dianthus species being seen everywhere in our...
The global rise of drug resistant tuberculosis has highlighted the need for improved diagnostic technologies that provide rapid and reliable drug resistance results. Here, we develop and validate a whole genome sequencing (WGS)-based test for identif...
Infectious laryngotracheitis virus (ILTV) is a herpes virus that causes an acute respiratory disease of poultry known as infectious laryngotracheitis (ILT). Chicken embryo origin (CEO) and tissue culture origin (TCO) live attenuated vaccines are rout...
Ganoderma lucidum is an important medicinal mushroom widely cultured in Asian countries. Exopolysaccharides are bioactive compounds of G. lucidum with health benefits. Limited exopolysaccharide content hinders its extraction from G. lucidum. The addi...
In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and compar...
Orientia tsutsugamushi is an obligate intracellular bacterium associated with trombiculid mites and is the causative agent of scrub typhus, a life-threatening febrile disease. Strain typing of O. tsutsugamushi is based on its immunodominant surface a...
The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,3...
Background: Copy number variants of uncertain significance (CNVus) from chromosome microarray analysis (CMA) presents unresolved challenges for clinical geneticists, genetic counselors, and patients. We performed a systematic reevaluation of reported...
Idiopathic superior oblique muscle palsy is a major type of paralytic, non-comitant strabismus and presents vertical and cyclo-torsional deviation of one eye against the other eye, with a large vertical fusion range and abnormal head posture such as...
Powassan virus (POWV) is an emerging tick-borne virus that causes severe meningoencephalitis in the United States, Canada, and Russia. Serology is generally the preferred diagnostic modality, but PCR on cerebrospinal fluid, blood, or urine has an imp...
The family of Ustilaginaceae belongs to the order of Basidiomycetes. Despite their plant pathogenicity causing, e.g., corn smut disease, they are also known as natural producers of value-added chemicals such as extracellular glycolipids, organic acid...
Whole-genome sequencing (WGS) is an increasingly adopted platform for predicting drug resistance in Mycobacterium tuberculosis; however, diagnostic accuracy varies substantially across bioinformatic tools and analytical frameworks, generating conside...
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