A5049246356- Cytomegalovirus and herpesvirus research
- Viral-associated cancers and disorders
- Herpesvirus Infections and Treatments
- Bacteriophages and microbial interactions
- Cancer-related molecular mechanisms research
- Poxvirus research and outbreaks
- Animal Disease Management and Epidemiology
- Animal Virus Infections Studies
- Virus-based gene therapy research
- Genomics and Phylogenetic Studies
- Plant and Fungal Interactions Research
- Viral Infections and Immunology Research
- Plant Virus Research Studies
- Molecular Biology Techniques and Applications
- Mosquito-borne diseases and control
- RNA modifications and cancer
- Insect Resistance and Genetics
- Viral Infections and Vectors
- RNA and protein synthesis mechanisms
- Viral Infectious Diseases and Gene Expression in Insects
- Vector-Borne Animal Diseases
- Advanced biosensing and bioanalysis techniques
- Hepatitis B Virus Studies
- Insect symbiosis and bacterial influences
- Entomopathogenic Microorganisms in Pest Control
University of Szeged
2019-2025
Mississippi State University
2021
Kaposi's sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with various high-throughput RNA-sequencing approaches map transcription start and end sites, splice junctions, translation initiation sites. Despite these efforts, comprehensive annotation of viral transcriptome remains incomplete. In present study, we generated long-read sequencing data set lytic latent using native RNA direct...
ABSTRACT Caviid gammaherpesvirus 1 (CaGHV-1), formerly known as the guinea pig herpes-like virus, is an oncogenic with a sequenced genome but as-yet uncharacterized transcriptome. Using nanopore long-read RNA sequencing, we annotated CaGHV-1 and constructed detailed transcriptomic atlas. Our findings reveal diverse viral mRNAs non-coding RNAs, along mapped promoter elements for each gene. We demonstrated that RTA lytic cycle transcription factor activates its own promoter, similar to...
Introduction Equid alphaherpesvirus 1 (EHV-1), a veterinary pathogen belonging to the Varicellovirus genus, is responsible for significant economic losses in global equine sector. This research involved timescale gene expression profiling and transcriptional reannotation of this herpesvirus. Methods We employed CAGE sequencing on Illumina platform determine transcript start sites, alongside long-read direct cDNA Oxford Nanopore Technology detect full-length viral transcripts. Samples were...
African swine fever virus (ASFV) is a large DNA belonging to the Asfarviridae family. Despite its agricultural importance, little known about fundamental molecular mechanisms of this pathogen. Short-read sequencing (SRS) can produce huge amount high-precision reads for transcriptomic profiling, but it inefficient comprehensively annotating transcriptomes. Long-read (LRS) overcome some SRS’s limitations, also has drawbacks, such as low-coverage and high error rate. The limitations two...
Epstein-Barr virus (EBV) is an important human pathogenic gammaherpesvirus with carcinogenic potential. The EBV transcriptome has previously been analyzed using both Illumina-based short read-sequencing and Pacific Biosciences RS II-based long-read sequencing technologies. Since the various methods have distinct strengths limitations, use of multiplatform approaches proven to be valuable. aim this study provide a more complete picture on transcriptomic architecture EBV.In work, we apply...
The recent human Monkeypox outbreak underlined the importance of studying basic biology orthopoxviruses. However, transcriptome its causative agent has not been investigated before neither with short-, nor long-read sequencing approaches. This Oxford Nanopore RNA-Sequencing dataset fills this gap. It will enable in-depth characterization transcriptomic architecture monkeypox virus, and may even make possible to annotate novel host transcripts. Moreover, our direct cDNA native RNA reads allow...
Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity various organisms, including viruses. Herpesviruses are known to produce range transcripts, either close or overlapping replication origins (Oris) and neighboring genes related transcription replication, which possess confirmed potential regulatory roles. In our research,...
DATA REPORT article Front. Genet., 28 July 2020Sec. Genomic Assay Technology Volume 11 - 2020 | https://doi.org/10.3389/fgene.2020.00758
Abstract Long-read sequencing (LRS) has become a standard approach for transcriptome analysis in recent years. Bovine alphaherpesvirus 1 (BoHV-1) is an important pathogen of cattle worldwide. This study reports the profiling dynamic lytic BoHV-1 using two long-read techniques, Oxford Nanopore Technologies MinION, and LoopSeq synthetic LRS methods, multiple library preparation protocols. In this work, we annotated viral mRNAs non-coding transcripts, large number transcript isoforms, including...
In this work, a long-read sequencing (LRS) technique based on the Oxford Nanopore Technology MinION platform was used for quantifying and kinetic characterization of poly(A) fraction bovine alphaherpesvirus type 1 (BoHV-1) lytic transcriptome across 12-h infection period. Amplification-based LRS techniques frequently generate artefactual transcription reads are biased towards production shorter amplicons. To avoid these undesired effects, we applied direct cDNA sequencing, an...
This study employed both short-read sequencing (SRS, Illumina) and long-read (LRS Oxford Nanopore Technologies) platforms to conduct a comprehensive analysis of the equid alphaherpesvirus 1 (EHV-1) transcriptome. The involved annotation canonical mRNAs their transcript variants, encompassing transcription start site (TSS) end (TES) isoforms, in addition alternative splicing forms. Furthermore, revealed presence numerous non-coding RNA (ncRNA) molecules, including intergenic antisense...
In the last couple of years, implementation long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity viral gene expression. this study, we carried out a systematic analysis on pseudorabies virus by combining our current data obtained using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION with earlier generated other LRS short-read techniques. As result, identified number novel genes, transcripts, transcript isoforms, including...
Long-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers major advantage over the earlier gold standard short-read in efficiency of identifying for example polycistronic transcript isoforms, including length- splice variants. In this work, we profile human cytomegalovirus transcriptome using two third-generation LRS platforms: Sequel from Pacific BioSciences, MinION Oxford Nanopore Technologies. We carried out both cDNA direct RNA sequencing,...
Abstract Objective In this study, we applied two long-read sequencing (LRS) approaches, including single-molecule real-time and nanopore-based methods to investigate the time-lapse transcriptome patterns of host gene expression as a response Vaccinia virus infection. Transcriptomes determined using short-read approaches are incomplete because these platforms inefficient or fail distinguish between polycistronic RNAs, transcript isoforms, transcriptional start sites, well readthroughs...
Third-generation sequencing is able to read full-length transcripts and thus efficiently identify RNA molecules transcript isoforms, including length splice isoforms. In this study, we report the time-course profiling of effect bovine alphaherpesvirus type 1 on gene expression epithelial cells using direct cDNA carried out MinION device Oxford Nanopore Technologies. These investigations revealed a substantial up- down-regulatory virus several networks host cells, those that are associated...
Viral transcriptomes that are determined using first- and second-generation sequencing techniques incomplete. Due to the short read length, these methods inefficient or fail distinguish between transcript isoforms, polycistronic RNAs, transcriptional overlaps readthroughs. Additionally, approaches insensitive for identification of splice start sites (TSSs) and, in most cases, end (TESs), especially isoforms with varying ends, multi-spliced transcripts. Long-read is able full-length nucleic...
In this study, two long-read sequencing (LRS) techniques, MinION from Oxford Nanopore Technologies and Sequel the Pacific Biosciences, were used for transcriptional characterization of a prototype baculovirus, Autographa californica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, thereby distinguish between transcript isoforms, mono- polycistronic RNAs, overlapping transcripts. Altogether, we detected 875 species, which 759 novel 116 annotated previously. These...
DATA REPORT article Front. Genet., 07 April 2021 | https://doi.org/10.3389/fgene.2021.619056
<title>Abstract</title> A member of the Varicellovirus genus herpesviruses, equid alphaherpesvirus 1 (EHV-1) was subjected to timescale profiling in this research. We employed cap analysis gene expression sequencing (CAGE-Seq) on Illumina platform determine transcript start sites alongside long-read direct cDNA (dcDNA-Seq) Oxford Nanopore Technology detect full-length viral transcripts. Samples were collected at nine distinct stages lifecycle, with triplicates taken each stage. also applied...
ABSTRACT Caviid gammaherpesvirus 1 (CaGHV-1), formerly known as the guinea pig herpes-like virus, is an oncogenic with a sequenced genome but as-yet uncharacterized transcriptome. Using nanopore long-read RNA sequencing, we annotated CaGHV-1 and constructed detailed transcriptomic atlas. Our findings reveal diverse viral mRNAs non-coding RNAs, along mapped promoter elements for each gene. We demonstrated that RTA lytic cycle transcription factor activates its own promoter, similar to KSHV,...
ABSTRACT Kaposi’s sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with various high-throughput RNA-sequencing approaches map transcription start and end sites, splice junctions, translation initiation sites. Despite these efforts, comprehensive annotation of viral transcriptome remains incomplete. In present study, we generated long-read sequencing dataset lytic latent using native RNA direct...
In this study, a structural profiling of equid alphaherpesvirus 1 (EHV-1) transcriptome was carried out using next-generation (Illumina) and third-generation (Oxford Nanopore Technologies) sequencing platforms. We annotated the canonical mRNA molecules their isoforms, including transcript start end site splice variants. Additionally, number putative 5′-truncated mRNAs containing shorter in-frame ORFs were detected. also demonstrated that EHV-1 produces high non-coding transcripts, antisense...
In the last couple of years, implementation long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity viral gene expression. this study, we carried out a systematic analysis on pseudorabies virus by combining our current data obtained using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencings with earlier generated other LRS short-read techniques. As result, identified number novel genes, transcripts, transcript...