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PubMed2025

A dedicated caller for DUX4 rearrangements from whole-genome sequencing data.

Rearrangements involving the DUX4 gene (DUX4-r) define a subtype of paediatric and adult acute lymphoblastic leukaemia (ALL) with a favourable outcome. Currently, there is no 'standard of care' diagnostic method for their confident identification. Here, we present an open-source software tool designed to detect DUX4-r from short-read, whole-genome sequencing (WGS) data. Evaluation on a cohort of 210 paediatric ALL cases showed that our method detects all known, as well as previously unidentified, cases of IGH::DUX4 and rearrangements with other partner genes. These findings demonstrate the possibility of robustly detecting DUX4-r using WGS in the routine clinical setting.

Humans↗

PubMed1994

Automated fluorescent genomic sequencing as applied to the methylation analysis of the human ornithine decarboxylase gene.

A genomic sequencing method for an automated DNA sequencer was developed. The method described here is an improved version of the previously published protocol, which utilizes bisulfite-induced modification of genomic DNA. In our method, the modified DNA is purified without a time-consuming dialysis, and the subsequent 2-step DNA amplification is carried out with one biotinylated primer in order to separate and isolate the strands of the product with the aid of streptavidin-coated magnetic beads. The strands are then sequenced with fluorescent primers and automated DNA sequencer. This provides means to determine reliably the methylation status of cytosines as well as the degree of methylation in a given CpG, site of the target sequence. The method was successfully applied to analyze the promoter region and the 11th exon of the human ornithine decarboxylase ODC gene in various human myeloma cell lines. The study revealed a totally unmethylated promoter region in every cell line studied, whereas the protein coding region appeared to be extensively methylated, although a dexamethasone resistant cell line displayed demethylation in certain CpG sequences. Also, a previously unknown ODC allele was detected.

Automation↗

PubMed2025

Whole-Genome Sequencing of 54 Dengchuan Cattle (Bos taurus) from Southwest China.

Domestic cattle (Bos taurus) play a significant role in human society as they provide abundant food resources and contribute to the development of agriculture and traditional culture. Dengchuan cattle, a local breed from Yunnan, Southwest China, are known for their high-quality milk and are at risk of extinction due to crossbreeding. To preserve the superior genetic resources of Dengchuan cattle, this study conducted whole-genome sequencing of 54 Dengchuan cattle using blood DNA samples, generating approximately 3.56 TB of clean data with an average sequencing depth of 32.78X. The sequencing data were aligned to the bovine reference genome (ARS-UCD2.0), achieving an average alignment rate of 99.85%. A total of 9,950,420 SNPs and 2,476,207 indels were detected using variant calling workflow. These data were utilized to characterize genomic profile of this unique cattle breed. The data generated in this study can be incorporated into the global cattle genomic diversity database, providing valuable information for comparative studies on cattle.

Animals↗

PubMed1988

Genome sequences of a mouse-avirulent and a mouse-virulent strain of Ross River virus.

The nucleotide sequence of the genomic RNA of a mouse-avirulent strain of Ross River virus, RRV NB5092 (isolated in 1969), has been determined and the corresponding sequence for the prototype mouse-virulent strain, RRV T48 (isolated in 1959), has been completed. The RRV NB5092 genome is approximately 11,674 nucleotides in length, compared with 11,853 nucleotides for RRV T48. RRV NB5092 and RRV T48 have the same genome organization. For both viruses an untranslated region of 80 nucleotides at the 5' end of the genome is followed by a 7440-nucleotide open reading frame which is interrupted after 5586 nucleotides by a single opal termination codon. By homology with other alphaviruses, the 5586-nucleotide open reading frame encodes the nonstructural proteins nsP1, nsP2, and nsP3; a fourth nonstructural protein, nsP4, is produced by read-through of the opal codon. The RRV nonstructural proteins show strong homology with the corresponding proteins of Sindbis virus and Semliki Forest virus in terms of size, net charge, and hydropathy characteristics. However, homology is not uniform between or within the proteins; nsP1, nsP2, and nsP4 contain extended domains which are highly conserved between alphaviruses, while the C-terminal region of nsP3 shows little conservation in sequence or length between alphaviruses. An untranslated "junction" region of 44 nucleotides (for RRV NB5092) or 47 nucleotides (for RRV T48) separates the nonstructural and structural protein coding regions. The structural proteins (capsid-E3-E2-6K-E1) are translated from an open reading frame of 3762 nucleotides which is followed by a 3'-untranslated region of approximately 348 nucleotides (for RRV NB5092) or 524 nucleotides (for RRV T48). Excluding deletions and insertions, the genomes of RRV NB5092 and RRV T48 differ at 284 nucleotides, representing a sequence divergence of 2.38%. Sequence deletions or insertions were found only in the noncoding regions and include a 173-nucleotide deletion in the 3'-untranslated region of RRV NB5092, compared with RRV T48. In the coding regions, most of the nucleotide differences are silent; there are 36 amino acid differences in the nonstructural proteins and 12 in the structural proteins. The distribution of amino acid differences between the two RRV strains correlates with the location of domains which are poorly conserved in sequence between alphaviruses. The possible role of amino acid differences in envelope glycoproteins E1 and E2 in determining the different antigenic and biological properties of RRV NB5092 and RRV T48 is discussed.

Alphavirus↗

PubMed2026

Genome sequences of four bacterial strains isolated from the phyllosphere of Mangifera indica trees in the polluted tropical city of Medellín, Colombia.

Complete and draft genome sequences of four phyllosphere-associated bacterial strains (Microbacterium radiodurans, Brachybacterium rhamnosum, Sphingomonas citri, and Curtobacterium sp.) isolated from Mangifera indica leaves in polluted Medellín, Colombia, are presented. These resources enable future studies on plant-microbe interactions and phyllosphere microbial mediation of atmospheric pollutants under urban stress.

Mangifera indica↗

PubMed1996

The genome sequence of the virulent Kabete 'O' strain of rinderpest virus: comparison with the derived vaccine.

We have compared the complete genome sequences of the vaccine strain of rinderpest virus and the virulent strain from which it was derived. Only 87 bases differed between the two genomes (0.55%). Possibly significant differences in amino acid sequence were found in the N, P, F, H and L proteins. A number of differences were also found in the leader region (3' end of the genome), whilst the trailer region appears to be more conserved. In addition, the length of the genome was found in both cases to be 15882, an exact multiple of six, fulfilling predictions made earlier based on work with Sendai and measles viruses.

Base Sequence↗

PubMed1998

The genomic sequences bound to special AT-rich sequence-binding protein 1 (SATB1) in vivo in Jurkat T cells are tightly associated with the nuclear matrix at the bases of the chromatin loops.

Special AT-rich sequence-binding protein 1 (SATB1), a DNA-binding protein expressed predominantly in thymocytes, recognizes an ATC sequence context that consists of a cluster of sequence stretches with well-mixed A's, T's, and C's without G's on one strand. Such regions confer a high propensity for stable base unpairing. Using an in vivo cross-linking strategy, specialized genomic sequences (0.1-1. 1 kbp) that bind to SATB1 in human lymphoblastic cell line Jurkat cells were individually isolated and characterized. All in vivo SATB1-binding sequences examined contained typical ATC sequence contexts, with some exhibiting homology to autonomously replicating sequences from the yeast Saccharomyces cerevisiae that function as replication origins in yeast cells. In addition, LINE 1 elements, satellite 2 sequences, and CpG island-containing DNA were identified. To examine the higher-order packaging of these in vivo SATB1-binding sequences, high-resolution in situ fluorescence hybridization was performed with both nuclear "halos" with distended loops and the nuclear matrix after the majority of DNA had been removed by nuclease digestion. In vivo SATB1-binding sequences hybridized to genomic DNA as single spots within the residual nucleus circumscribed by the halo of DNA and remained as single spots in the nuclear matrix, indicating that these sequences are localized at the base of chromatin loops. In human breast cancer SK-BR-3 cells that do not express SATB1, at least one such sequence was found not anchored onto the nuclear matrix. These findings provide the first evidence that a cell type-specific factor such as SATB1 binds to the base of chromatin loops in vivo and suggests that a specific chromatin loop domain structure is involved in T cell-specific gene regulation.

Base Composition↗

PubMed2025

Whole genome sequencing analysis of Candida glabrata isolates collected from patients with selected drug-resistant candidiasis hospitalized in Eastern Poland.

The epidemiology data for candidiasis indicate an increase in Candida glabrata infections. Moreover, several reports have shown an increasing number of drug-resistant cases of these infections. The source of drug resistance can often be traced to genetic mutations in genes related to a drug's mechanism of action. Therefore, we conducted whole genome sequencing of several drug-resistant isolates of Candida glabrata collected from patients hospitalized in Eastern Poland to assess whether mutations in selected genes correlated with susceptibility analysis results. The fungal species from patient samples were identified, and the isolated Candida glabrata were subjected to antifungal drug susceptibility testing. The results were interpreted according to the EUCAST and CLSI recommendations. Susceptibility to 5-flucytosine was assessed using the ATB FUNGUS kit. Libraries were prepared according to the NEXTERA XT DNA Library Prep and subsequently sequenced. The outcomes indicated common resistance to two of the three analyzed echinocandins, as well as two cases of simultaneous resistance to echinocandins and selected azole-based drugs. We detected several previously reported mutations in selected resistance-related genes, as well as five that are first described here: ERG5 (M267I), ERG6 (R57K), PDH1 (K438Q, V434I, F600V, V1192S), FCY1 (M129T), and FCY2 (I384F). Neither of the identified nonsynonymous mutations was correlated with the drug resistance demonstrated in the susceptibility testing. Furthermore, we can exclude the possibility of acquired drug resistance, thereby raising questions about the possibility of unknown mechanisms of resistance to azole-based and echinocandin drugs.

Candida glabrata↗

PubMed1990

Detection of measles virus genomic sequences in SSPE brain tissue by the polymerase chain reaction.

The polymerase chain reaction (PCR) was modified to detect RNA genomic sequences by generating cDNA copies of these sequences as a preliminary step. Oligonucleotide primer pairs complementary to sequences in each of the five major structural protein genes of the measles virus (nucleocapsid protein, phosphoprotein, matrix protein, fusion protein, and hemagglutinin protein) were synthesized. PCR products were tentatively identified by visualization of bands of the appropriate size by ethidium bromide staining after gel electrophoresis, and identity was confirmed by subsequent restriction enzyme cleavage of the products at predetermined sites to yield fragments of predicted size. This method successfully amplified 400-500 base regions from each of these five genes in RNA extracts of wild measles virus cultured in Vero cells and in RNA extracted from most of the SSPE brain tissues tested, but not in RNA from any control brain tissues. Measles virus genome was detected in SSPE brain tissues stored frozen for as long as 27 years and formalin-fixed paraffin-embedded subacute sclerosing panencephalitis (SSPE) brain tissues as old as 9 years. This method provides a simple, rapid and highly sensitive means of detecting and identifying sequences of RNA genomes by PCR. The success of this method in detecting measles virus in SSPE brain tissue suggests that PCR is appropriate to investigate the possible presence of RNA viruses in other neurological disorders of unknown etiology.

Adolescent↗

PubMed2003

Complete genomic sequence of Pepper vein banding virus (PVBV): a distinct member of the genus Potyvirus.

The complete genomic sequence of Pepper vein banding virus (PVBV), a potyvirus infecting chilli and other solanaceous plants in south India, was determined and compared with those of other potyviruses. The viral genome contained 9711 nucleotides, excluding the poly-A tail. The length of the 5'- and 3'-untranslated regions (UTR) were 163 and 281 nucleotides respectively. As for other potyviruses, the PVBV genome has a single open reading frame (ORF) starting at nucleotide 164 and ending at nt 9430, which encodes a polyprotein of 3088 amino acid residues. There are nine putative conserved cleavage sites within the polyprotein, which can result in ten functionally distinct protein products. Phylogenetic analysis of the potyviral polyprotein sequences showed that PVBV is a distinct species of this genus.

Capsicum↗

PubMed2000

Analysis of the complete genome sequence of acute bee paralysis virus shows that it belongs to the novel group of insect-infecting RNA viruses.

The complete genome sequence of acute bee paralysis virus (ABPV) was determined. The 9470 nucleotide, polyadenylated RNA genome encoded two open reading frames (ORF1 and ORF2), which were separated by 184 nucleotides. The deduced amino acid sequence of the 5' ORF1 (nucleotides 605 to 6325) showed significant similarity to the RNA-dependent RNA polymerase, helicase, and protease domains of viruses from the picornavirus, comovirus, calicivirus, and sequivirus families, as well as to a novel group of insect-infecting RNA viruses. The 3' ORF2 (nucleotides 6509-9253) was proposed as encoding a capsid polyprotein with three major structural proteins (35, 33, and 24 kDa) and a minor protein (9.4 kDa). This was confirmed by N-terminal sequence analysis of two of these proteins. The overall genome structure of ABPV showed similarities to those of Drosophila C virus, Plautia stali intestine virus, Rhopalosiphum padi virus, and Himetobi P virus, which have been classified into a novel group of picorna-like insect-infecting RNA viruses called cricket paralysis-like viruses. It is suggested that ABPV belongs to the cricket paralysis-like viruses.

Amino Acid Sequence↗

PubMed2026

Genome-sequencing-based benchmarking of antimicrobial resistance, treatment outcomes and healthcare transmission events for Clostridioides difficile infection in Australian hospitals.

BACKGROUND: Clostridioides difficile infection (CDI) remains a priority for infection prevention and control in health care, particularly with the emergence of hypervirulent strains and antimicrobial resistance (AMR). AIM: To characterize the genomic epidemiology and AMR profiles of culture-confirmed CDI cases within tertiary hospitals in Australia. METHODS: A total of 155 C. difficile isolates from 142 patients with CDI diagnosed in four hospitals between 2023 and 2025 were studied. Data collected included patient demographics, severity of infection, antibiotic treatment and clinical outcomes at 8 weeks. Phenotypic susceptibility to vancomycin, fidaxomicin, metronidazole, moxifloxacin, meropenem, tetracycline and rifaximin were determined by agar dilution. Isolates underwent whole-genome sequencing (WGS) for genotyping and resistome assessment. FINDINGS: WGS differentiated 39 distinct sequence types among CDI isolates across different healthcare services. In total, 100 isolates were singletons and 55 (35% clustering rate) isolates were considered to be genomically related (difference of two or fewer single-nucleotide polymorphisms). Of these, 12 patients (8.5%) with close hospital contact formed six epidemiologically linked clusters. Phenotypic susceptibility results were obtained for 134 (86.4%) CDI isolates. There was no phenotypic resistance to vancomycin [minimum inhibitory concentration required to inhibit the growth of 90% of isolates (MIC90) 1 mg/L], metronidazole (MIC90 0.5 mg/L) or fidaxomicin (MIC90 0.5 mg/L). There was no association in the study cohort between the presence of resistance genes or reduced phenotypic susceptibility and CDI recurrence. CONCLUSION: Genomic analysis of C. difficile isolates did not identify any outbreaks or an association between the sequence type or presence of a resistance gene and clinical outcomes. High-resolution characterization and identification of antibiotic resistance, CDI clinical relapse and recent transmission offered by genome sequencing can provide important benchmarks for hospital infection control.

Antibiotic resistance↗

PubMed2005

Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.

Corynebacterium jeikeium is a "lipophilic" and multidrug-resistant bacterial species of the human skin flora that has been recognized with increasing frequency as a serious nosocomial pathogen. Here we report the genome sequence of the clinical isolate C. jeikeium K411, which was initially recovered from the axilla of a bone marrow transplant patient. The genome of C. jeikeium K411 consists of a circular chromosome of 2,462,499 bp and the 14,323-bp bacteriocin-producing plasmid pKW4. The chromosome of C. jeikeium K411 contains 2,104 predicted coding sequences, 52% of which were considered to be orthologous with genes in the Corynebacterium glutamicum, Corynebacterium efficiens, and Corynebacterium diphtheriae genomes. These genes apparently represent the chromosomal backbone that is conserved between the four corynebacteria. Among the genes that lack an ortholog in the known corynebacterial genomes, many are located close to transposable elements or revealed an atypical G+C content, indicating that horizontal gene transfer played an important role in the acquisition of genes involved in iron and manganese homeostasis, in multidrug resistance, in bacterium-host interaction, and in virulence. Metabolic analyses of the genome sequence indicated that the "lipophilic" phenotype of C. jeikeium most likely originates from the absence of fatty acid synthase and thus represents a fatty acid auxotrophy. Accordingly, both the complete gene repertoire and the deduced lifestyle of C. jeikeium K411 largely reflect the strict dependence of growth on the presence of exogenous fatty acids. The predicted virulence factors of C. jeikeium K411 are apparently involved in ensuring the availability of exogenous fatty acids by damaging the host tissue.

Anti-Bacterial Agents↗

PubMed2001

Indexing huge genome sequences for solving various problems.

Because of the increase in the size of genome sequence databases, the importance of indexing the sequences for fast queries grows. Suffix trees and suffix arrays are used for simple queries. However these are not suitable for complicated queries from huge amount of sequences because the indices are stored in disk which has slow access speed. We propose storing the indices in memory in a compressed form. We use the compressed suffix array. It compactly stores the suffix array at the cost of theoretically a small slowdown in access speed. We experimentally show that the overhead of using the compressed suffix array is reasonable in practice. We also propose an approximate string matching algorithm which is suitable for the compressed suffix array. Furthermore, we have constructed the compressed suffix array of the whole human genome. Because its size is about 2G bytes, a workstation can handle the search index for the whole data in main memory, which will accelerate the speed of solving various problems in genome informatics.

Abstracting and Indexing↗

PubMed2006

GenRGenS: software for generating random genomic sequences and structures.

SUMMARY: GenRGenS is a software tool dedicated to randomly generating genomic sequences and structures. It handles several classes of models useful for sequence analysis, such as Markov chains, hidden Markov models, weighted context-free grammars, regular expressions and PROSITE expressions. GenRGenS is the only program that can handle weighted context-free grammars, thus allowing the user to model and to generate structured objects (such as RNA secondary structures) of any given desired size. GenRGenS also allows the user to combine several of these different models at the same time.

Computational Biology↗

PubMed2026

The coding-complete genome sequence of Arabidopsis latent virus 1 from Iraq.

Here, we report the coding-complete genome sequence of Arabidopsis latent virus 1 (ArLV1; Comovirus arabidopsis) from Iraq. The virus was identified by metatranscriptomic sequencing of asymptomatic cucumber (Cucumis sativus) leaves harboring thrips collected from commercial greenhouses. The bipartite genome comprises RNA1 (5,553 nt) and RNA2 (3,582 nt).

Arabidopsis latent virus 1↗

PubMed2005

Amplification of genomic sequences flanking T-DNA insertions by thermal asymmetric interlaced polymerase chain reaction.

Thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) is an efficient tool for the recovery of DNA fragments adjacent to known sequences. A protocol is presented for the amplification of genomic sequences flanking DNA (T-DNA or transposon) insertions using the TAIL-PCR method. The amplified products are suitable as templates for direct sequencing, or for cloning in vectors. Examples are given in use of the protocol for T-DNA tagging in rice using the pCAMBIA binary vectors.

Base Sequence↗

PubMed2026

Complete genome sequence of the Anaplasma phagocytophilum clinical isolate NCH-1.

Anaplasma phagocytophilum is an obligate intracellular gram-negative bacterium and etiologic agent of human granulocytic anaplasmosis. A. phagocytophilum genomic sequencing has historically been performed via short-read platforms. Our optimized bacterial isolation protocol combined with Nanopore sequencing produced a single, closed 1,481,805 bp circular A. phagocytophilum strain NCH-1 chromosome.

Anaplasma phagocytophilum↗