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Anguillid herpesvirus 1 transcriptome

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Anguillid herpesvirus 1 transcriptome. / van Beurden, Steven J.; Gatherer, Derek; Kerr, Karen et al.

In: Journal of Virology, Vol. 86, No. 18, 09.2012, p. 10150-10161.

Research output: Contribution to Journal/MagazineJournal articlepeer-review

Harvard

van Beurden, SJ, Gatherer, D, Kerr, K, Galbraith, J, Herzyk, P, Peeters, BPH, Engelsma, MY, Rottier, PJM & Davison, AJ 2012, 'Anguillid herpesvirus 1 transcriptome', Journal of Virology, vol. 86, no. 18, pp. 10150-10161. https://doi.org/10.1128/JVI.01271-12

APA

van Beurden, S. J., Gatherer, D., Kerr, K., Galbraith, J., Herzyk, P., Peeters, B. P. H., Engelsma, M. Y., Rottier, P. J. M., & Davison, A. J. (2012). Anguillid herpesvirus 1 transcriptome. Journal of Virology, 86(18), 10150-10161. https://doi.org/10.1128/JVI.01271-12

Vancouver

van Beurden SJ, Gatherer D, Kerr K, Galbraith J, Herzyk P, Peeters BPH et al. Anguillid herpesvirus 1 transcriptome. Journal of Virology. 2012 Sep;86(18):10150-10161. doi: 10.1128/JVI.01271-12

Author

van Beurden, Steven J. ; Gatherer, Derek ; Kerr, Karen et al. / Anguillid herpesvirus 1 transcriptome. In: Journal of Virology. 2012 ; Vol. 86, No. 18. pp. 10150-10161.

Bibtex

@article{40609232e1d845bd9b03d6f1240e3cce,
title = "Anguillid herpesvirus 1 transcriptome",
abstract = "We used deep sequencing of poly(A) RNA to characterize the transcriptome of an economically important eel virus, anguillid herpesvirus 1 (AngHV1), at a stage during the lytic life cycle when infectious virus was being produced. In contrast to the transcription of mammalian herpesviruses, the overall level of antisense transcription from the 248,526-bp genome was low, amounting to only 1.5% of transcription in predicted protein-coding regions, and no abundant, nonoverlapping, noncoding RNAs were identified. RNA splicing was found to be more common than had been anticipated previously. Counting the 10,634-bp terminal direct repeat once, 100 splice junctions were identified, of which 58 were considered likely to be involved in the expression of functional proteins because they represent splicing between protein-coding exons or between 5' untranslated regions and protein-coding exons. Each of the 30 most highly represented of these 58 splice junctions was confirmed by RT-PCR. We also used deep sequencing to identify numerous putative 5' and 3' ends of AngHV1 transcripts, confirming some and adding others by rapid amplification of cDNA ends (RACE). The findings prompted a revision of the AngHV1 genome map to include a total of 129 protein-coding genes, 5 of which are duplicated in the terminal direct repeat. Not counting duplicates, 11 genes contain integral, spliced protein-coding exons, and 9 contain 5' untranslated exons or, because of alternative splicing, 5' untranslated and 5' translated exons. The results of this study sharpen our understanding of AngHV1 genomics and provide the first detailed view of a fish herpesvirus transcriptome.",
keywords = "Anguilla, Animals, Base Sequence, Cells, Cultured, Chromosome Mapping, Gene Library, Genome, Viral, Herpesviridae, RNA Splice Sites, RNA, Viral, Transcriptome",
author = "{van Beurden}, {Steven J.} and Derek Gatherer and Karen Kerr and Julie Galbraith and Pawel Herzyk and Peeters, {Ben P. H.} and Engelsma, {Marc Y.} and Rottier, {Peter J. M.} and Davison, {Andrew J.}",
year = "2012",
month = sep,
doi = "10.1128/JVI.01271-12",
language = "English",
volume = "86",
pages = "10150--10161",
journal = "Journal of Virology",
issn = "0022-538X",
publisher = "American Society for Microbiology",
number = "18",

}

RIS

TY - JOUR

T1 - Anguillid herpesvirus 1 transcriptome

AU - van Beurden, Steven J.

AU - Gatherer, Derek

AU - Kerr, Karen

AU - Galbraith, Julie

AU - Herzyk, Pawel

AU - Peeters, Ben P. H.

AU - Engelsma, Marc Y.

AU - Rottier, Peter J. M.

AU - Davison, Andrew J.

PY - 2012/9

Y1 - 2012/9

N2 - We used deep sequencing of poly(A) RNA to characterize the transcriptome of an economically important eel virus, anguillid herpesvirus 1 (AngHV1), at a stage during the lytic life cycle when infectious virus was being produced. In contrast to the transcription of mammalian herpesviruses, the overall level of antisense transcription from the 248,526-bp genome was low, amounting to only 1.5% of transcription in predicted protein-coding regions, and no abundant, nonoverlapping, noncoding RNAs were identified. RNA splicing was found to be more common than had been anticipated previously. Counting the 10,634-bp terminal direct repeat once, 100 splice junctions were identified, of which 58 were considered likely to be involved in the expression of functional proteins because they represent splicing between protein-coding exons or between 5' untranslated regions and protein-coding exons. Each of the 30 most highly represented of these 58 splice junctions was confirmed by RT-PCR. We also used deep sequencing to identify numerous putative 5' and 3' ends of AngHV1 transcripts, confirming some and adding others by rapid amplification of cDNA ends (RACE). The findings prompted a revision of the AngHV1 genome map to include a total of 129 protein-coding genes, 5 of which are duplicated in the terminal direct repeat. Not counting duplicates, 11 genes contain integral, spliced protein-coding exons, and 9 contain 5' untranslated exons or, because of alternative splicing, 5' untranslated and 5' translated exons. The results of this study sharpen our understanding of AngHV1 genomics and provide the first detailed view of a fish herpesvirus transcriptome.

AB - We used deep sequencing of poly(A) RNA to characterize the transcriptome of an economically important eel virus, anguillid herpesvirus 1 (AngHV1), at a stage during the lytic life cycle when infectious virus was being produced. In contrast to the transcription of mammalian herpesviruses, the overall level of antisense transcription from the 248,526-bp genome was low, amounting to only 1.5% of transcription in predicted protein-coding regions, and no abundant, nonoverlapping, noncoding RNAs were identified. RNA splicing was found to be more common than had been anticipated previously. Counting the 10,634-bp terminal direct repeat once, 100 splice junctions were identified, of which 58 were considered likely to be involved in the expression of functional proteins because they represent splicing between protein-coding exons or between 5' untranslated regions and protein-coding exons. Each of the 30 most highly represented of these 58 splice junctions was confirmed by RT-PCR. We also used deep sequencing to identify numerous putative 5' and 3' ends of AngHV1 transcripts, confirming some and adding others by rapid amplification of cDNA ends (RACE). The findings prompted a revision of the AngHV1 genome map to include a total of 129 protein-coding genes, 5 of which are duplicated in the terminal direct repeat. Not counting duplicates, 11 genes contain integral, spliced protein-coding exons, and 9 contain 5' untranslated exons or, because of alternative splicing, 5' untranslated and 5' translated exons. The results of this study sharpen our understanding of AngHV1 genomics and provide the first detailed view of a fish herpesvirus transcriptome.

KW - Anguilla

KW - Animals

KW - Base Sequence

KW - Cells, Cultured

KW - Chromosome Mapping

KW - Gene Library

KW - Genome, Viral

KW - Herpesviridae

KW - RNA Splice Sites

KW - RNA, Viral

KW - Transcriptome

U2 - 10.1128/JVI.01271-12

DO - 10.1128/JVI.01271-12

M3 - Journal article

C2 - 22787220

VL - 86

SP - 10150

EP - 10161

JO - Journal of Virology

JF - Journal of Virology

SN - 0022-538X

IS - 18

ER -