A5043993080- Cytomegalovirus and herpesvirus research
- Herpesvirus Infections and Treatments
- Viral-associated cancers and disorders
- Plant Virus Research Studies
- Bacteriophages and microbial interactions
- Animal Virus Infections Studies
- Plant and Fungal Interactions Research
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Poxvirus research and outbreaks
- Animal Disease Management and Epidemiology
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Virus-based gene therapy research
- Mosquito-borne diseases and control
- Viral Infections and Immunology Research
- Molecular Biology Techniques and Applications
- Vector-Borne Animal Diseases
- Viral Infectious Diseases and Gene Expression in Insects
- RNA Research and Splicing
- Insect Resistance and Genetics
- interferon and immune responses
- RNA regulation and disease
- SARS-CoV-2 detection and testing
- Gut microbiota and health
University of Szeged
2016-2025
Mississippi State University
2021
Stanford University
2019
HUN-REN Szegedi Biológiai Kutatóközpont
2013
Hungarian Academy of Sciences
2013
Institute of Biochemistry
2013
Whole transcriptome studies have become essential for understanding the complexity of genetic regulation. However, conventionally applied short-read sequencing platforms cannot be used to reliably distinguish between many transcript isoforms. The Pacific Biosciences (PacBio) RS II platform is capable reading long nucleic acid stretches in a single run. pseudorabies virus (PRV) an excellent system study herpesvirus gene expression and potential interactions transcriptional units. In this...
In this study, we used the amplified isoform sequencing technique from Pacific Biosciences to characterize poly(A)+ fraction of lytic transcriptome herpes simplex virus type 1 (HSV-1). Our analysis detected 34 formerly unidentified protein-coding genes, ten non-coding RNAs, as well 17 polycistronic and complex transcripts. This work also led us identify many transcript isoforms, including 13 splice 68 end variants, several overlaps. Additionally, determined previously unascertained...
The human cytomegalovirus (HCMV) is a ubiquitous, pathogenic herpesvirus. complete viral genome transcriptionally active during infection; however, large part of its transcriptome has yet to be annotated. In this work, we applied the amplified isoform sequencing technique from Pacific Biosciences characterize lytic HCMV strain Towne varS. We developed pipeline for transcript annotation using long-read data. identified 248 transcriptional start sites, 116 termination sites and 80 splicing...
Third-generation sequencing is an emerging technology that capable of solving several problems earlier approaches were not able to, including the identification transcripts isoforms and overlapping transcripts. In this study, we used long-read for analysis pseudorabies virus (PRV) transcriptome, Oxford Nanopore Technologies MinION, PacBio RS-II, Illumina HiScanSQ platforms. We also data from our previous short-read studies comparison results in order to confirm obtained data. Our...
Varicella zoster virus (VZV) is a human pathogenic alphaherpesvirus harboring relatively large DNA molecule. The VZV transcriptome has already been analyzed by microarray and short-read sequencing analyses. However, both approaches have substantial limitations when used for structural characterization of transcript isoforms, even if supplemented with primer extension or other techniques. Among others, they are inefficient in distinguishing between embedded RNA molecules, including splice...
The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is an insect-pathogen baculovirus. In this study, we applied the Oxford Nanopore Technologies platform for analysis of polyadenylated fraction viral transcriptome using both cDNA and direct RNA sequencing methods. We identified annotated altogether 132 novel transcripts transcript isoforms, including 4 coding non-coding molecules, 47 length variants, 5 splice as well 23 polycistronic 49 complex transcripts. All protein-coding...
Abstract We carried out whole-exome ultra-high throughput sequencing in brain samples of suicide victims who had suffered from major depressive disorder and control subjects died other causes. This study aimed to reveal the selective accumulation rare variants coding UTR sequences within genes victims. also analysed potential effect STR CNV variations, as well infection with neurovirulent viruses this behavioural disorder. As a result, we have identified several candidate genes, among others...
Abstract Herpesvirus gene expression is co-ordinately regulated and sequentially ordered during productive infection. The viral genes can be classified into three distinct kinetic groups: immediate-early, early, late classes. In this study, a massively parallel sequencing technique that based on PacBio Single Molecule Real-time platform, was used for quantifying the poly(A) fraction of lytic transcriptome pseudorabies virus (PRV) throughout 12-hour interval infection PK-15 cells. Other...
Abstract Background Alternative polyadenylation is commonly examined using cDNA sequencing, which known to be affected by template-switching artifacts. However, the effects of such artifacts on alternative are generally disregarded, while attributed internal priming. Results Here, we analyzed both long-read sequencing and direct RNA data two organisms, generated different platforms. We developed a filtering algorithm takes into consideration that can source artifactual when out spurious...
Long-read sequencing (LRS) has become increasingly important in RNA research due to its strength resolving complex transcriptomic architectures. In this regard, currently two LRS platforms have demonstrated adequate performance: the Single Molecule Real-Time Sequencing by Pacific Biosciences (PacBio) and nanopore Oxford Nanopore Technologies (ONT). Even though these techniques produce lower coverage are more error prone than short-read sequencing, they continue be successful identifying...
In this study we identified two 3′-coterminal RNA molecules in the pseudorabies virus. The highly abundant short transcript (CTO-S) proved to be encoded between ul21 and ul22 genes close vicinity of replication origin (OriL) less long molecule (CTO-L) is a transcriptional readthrough product gene overlaps OriL. These polyadenylated RNAs were characterized by ascertaining their nucleotide sequences with Illumina HiScanSQ Pacific Biosciences Real-Time (PacBio RSII) sequencing platforms...
Pseudorabies virus is a widely-studied model organism of the Herpesviridae family, with compact genome arrangement 72 known coding sequences. In order to obtain an up-to-date genetic map virus, combination RNA-sequencing approaches were applied, as recent advancements in high-throughput sequencing methods have provided wealth information on novel RNA species and transcript isoforms, revealing additional layers transcriptome complexity several viral species. The total content polyadenylation...
ABSTRACT Pseudorabies virus (PRV) is a neurotropic herpesvirus that causes Aujeszky's disease in pigs. PRV strains are widely used as transsynaptic tracers for mapping neural circuits. We present here the complete and fully annotated genome sequence of strain Kaplan PRV, determined by Pacific Biosciences RSII long-read sequencing technology.
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...
Abstract In our research, we performed temporal transcriptomic profiling of host cells infected with Equid alphaherpesvirus 1 (EHV-1) by utilizing direct cDNA sequencing based on nanopore MinION technology. The reads were harnessed for transcript quantification at various time points. Viral infection-induced differential gene expression was identified through the edgeR package. genes segmented into six groups their kinetic characteristics. initial three clusters encompass immediate-early...
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...
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
Characterization of global transcriptomes using conventional short-read sequencing is challenging due to the insensitivity these platforms transcripts isoforms, multigenic RNA molecules, and transcriptional overlaps. Long-read (LRS) can overcome limitations by reading full-length transcripts. Employment technologies has led redefinition complexities in reported organisms. In this study, we applied LRS from Pacific Biosciences Oxford Nanopore Technologies profile vaccinia virus (VACV)...
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...
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...