Characterizing the Transcriptome of Turkey Hemorrhagic Enteritis Virus
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ABSTRACT:
PROVIDER: PRJNA1070351 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27777100_1.fastq.gz | Fastqsanger.gz | |||
| SRR27777100_2.fastq.gz | Fastqsanger.gz | |||
| SRR27777101_1.fastq.gz | Fastqsanger.gz | |||
| SRR27777101_2.fastq.gz | Fastqsanger.gz | |||
| SRR27777102_1.fastq.gz | Fastqsanger.gz |
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Project description:Characterizing the splice map of turkey hemorrhagic enteritis virus (THEV) is an essential step that would allow studies of individual genes mediating its immunosuppressive functions. We used an RNA-sequencing experiment to characterize the transcriptome of THEV for the first time, providing key insight into the THEV gene expression and mRNA structures. Researchers previously annotated the genome of THEV as encoding 23 open reading frames (ORFs). In this work we identified 29 spliced transcripts all of which consisted of novel exons although some exons matched some previously annotated ORFs. The three annotated splice junctions were also corroborated by our data. We performed PCR amplification of THEV cDNA, cloned the PCR products, and used Sanger sequencing to validate all identified splice junctions. During validation we identified five additional unique transcripts, a subset of which were further validated by 3' rapid amplification of cDNA ends (3' RACE) experiments. Thus, we report that the genome of THEV contains 34 transcripts with the coding capacity for all annotated ORFs. However, we found six of the previously annotated ORFs (ORF1, E3, 33K, ORF8, IVa2, and protease) to be truncated ORFs on the basis of the identification of an in-frame upstream start codon or the detection of additional coding exons. We also identified three of the annotated ORFs with longer or shorter isoforms, and seven novel unannotated ORFs that could potentially be translated; although it is beyond the scope of this manuscript to investigate whether they are translated. Similar to other adenoviruses (AdVs), THEV also produces multiple distinctly spliced transcripts that code for the same proteins across its genome. Our data show that all THEV transcripts are spliced and organized into five transcription units under the control of their cognate promoters like other AdVs.
2024-07-30 | GSE254416 | GEO
Project description:BackgroundHemorrhagic enteritis, caused by Turkey Hemorrhagic Enteritis Virus (THEV), is a disease affecting turkey poults characterized by immunosuppression and bloody diarrhea. An avirulent THEV strain that retains the immunosuppressive ability is used as a live vaccine. Characterizing the splice map of THEV is an essential step that would allow studies of individual genes mediating its immunosuppressive functions. We used RNA sequencing to characterize the splice map of THEV for the first time, providing key insights into the THEV gene expression and mRNA structures.MethodsAfter infecting a turkey B-cell line with the vaccine strain, samples in triplicates were collected at 4-, 12-, 24-, and 72-hours post-infection. Total RNA was extracted, and poly-A-tailed mRNA sequenced. Reads were mapped to the THEV genome after trimming and transcripts assembled with StringTie. We performed PCR of THEV cDNA, cloned the PCR products, and used Sanger sequencing to validate all identified splice junctions.ResultsResearchers previously annotated the THEV genome as encoding 23 open reading frames (ORFs). We identified 29 spliced transcripts from our RNA sequencing data, all containing novel exons although some exons matched some previously annotated ORFs. The three annotated splice junctions were also corroborated by our data. During validation we identified five additional unique transcripts, a subset of which were further validated by 3' rapid amplification of cDNA ends (3' RACE). Thus, we report that the genome of THEV contains 34 transcripts with the coding capacity for all annotated ORFs. However, we found six of the previously annotated ORFs to be truncated ORFs on the basis of the identification of an in-frame upstream start codon or the detection of additional coding exons. We also identified three of the annotated ORFs with longer or shorter isoforms, and seven novel unannotated ORFs that could potentially be translated; although it is beyond the scope of this manuscript to investigate whether they are translated.ConclusionsSimilar to human adenoviruses, all THEV transcripts are spliced and organized into five transcription units under the control of their cognate promoters. The genes are expressed under temporal regulation and THEV also produces multiple distinctly spliced transcripts that code for the same protein. Studies of the newly identified potential proteins should be urgently performed as these proteins may have roles in THEV-induced immunosuppression. Also, knowing the splicing of THEV genes should be invaluable to future research focusing on studying THEV genes, as this will allow accurate cloning of the mRNAs.
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2021-10-22 | GSE185797 | GEO
Project description:We describe here transcripts induced after intraperitoneal injection of rainbow trout with 2 different viruses, both belonging to strain 23.75 of viral hemorrhagic septicemia virus (VHSV): a deleted Nv gene (dNV) virus and a wild type (wt) virus. Two days after infection, differentially expressed transcript levels from selected immune-related trout genes were studied in internal organs (spleen and head kidney).
2015-03-05 | GSE43285 | GEO
Project description:We describe here transcripts induced after intraperitoneal injection of rainbow trout with 2 different viruses, both belonging to strain 23.75 of viral hemorrhagic septicemia virus (VHSV): a deleted Nv gene (dNV) virus and a wild type (wt) virus. Two days after infection, differentially expressed transcript levels from selected immune-related trout genes were studied in internal organs (spleen and head kidney). Fishes were divided in two groups (3 fishes per group). The first group was intraperitoneally injected with 100000 pfu per trout of dNV VHSV, while the second group was injected with 100000 pfu/trout of wt VHSV. All fishes were sacrificed two days post infection.
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