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Characterization of pseudorabies virus transcriptome by Illumina sequencing

Overview of attention for article published in BMC Microbiology, July 2015
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Title
Characterization of pseudorabies virus transcriptome by Illumina sequencing
Published in
BMC Microbiology, July 2015
DOI 10.1186/s12866-015-0470-0
Pubmed ID
Authors

Péter Oláh, Dóra Tombácz, Nándor Póka, Zsolt Csabai, István Prazsák, Zsolt Boldogkői

Abstract

Pseudorabies virus is a widely-studied model organism of the Herpesviridae family, with a compact genome arrangement of 72 known coding sequences. In order to obtain an up-to-date genetic map of the virus, a combination of RNA-sequencing approaches were applied, as recent advancements in high-throughput sequencing methods have provided a wealth of information on novel RNA species and transcript isoforms, revealing additional layers of transcriptome complexity in several viral species. The total RNA content and polyadenylation landscape of pseudorabies virus were characterized for the first time at high coverage by Illumina high-throughput sequencing of cDNA samples collected during the lytic infectious cycle. As anticipated, nearly all of the viral genome was transcribed, with the exception of loci in the large internal and terminal repeats, and several small intergenic repetitive sequences. Our findings included a small novel polyadenylated non-coding RNA near an origin of replication, and the single-base resolution mapping of 3' UTRs across the viral genome. Alternative polyadenylation sites were found in a number of genes and a novel alternative splice site was characterized in the ep0 gene, while previously known splicing events were confirmed, yielding no alternative splice isoforms. Additionally, we detected the active polyadenylation of transcripts earlier believed to be transcribed as part of polycistronic RNAs. To the best of our knowledge, the present work has furnished the highest-resolution transcriptome map of an alphaherpesvirus to date, and reveals further complexities of viral gene expression, with the identification of novel transcript boundaries, alternative splicing of the key transactivator EP0, and a highly abundant, novel non-coding RNA near the lytic replication origin. These advances provide a detailed genetic map of PRV for future research.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 30 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Italy 1 3%
Unknown 29 97%

Demographic breakdown

Readers by professional status Count As %
Student > Master 7 23%
Student > Ph. D. Student 5 17%
Student > Doctoral Student 2 7%
Researcher 2 7%
Student > Postgraduate 2 7%
Other 3 10%
Unknown 9 30%
Readers by discipline Count As %
Agricultural and Biological Sciences 9 30%
Biochemistry, Genetics and Molecular Biology 6 20%
Veterinary Science and Veterinary Medicine 2 7%
Medicine and Dentistry 2 7%
Immunology and Microbiology 1 3%
Other 1 3%
Unknown 9 30%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 24 July 2015.
All research outputs
#18,616,159
of 23,881,329 outputs
Outputs from BMC Microbiology
#2,087
of 3,286 outputs
Outputs of similar age
#180,027
of 265,842 outputs
Outputs of similar age from BMC Microbiology
#30
of 46 outputs
Altmetric has tracked 23,881,329 research outputs across all sources so far. This one is in the 19th percentile – i.e., 19% of other outputs scored the same or lower than it.
So far Altmetric has tracked 3,286 research outputs from this source. They receive a mean Attention Score of 4.2. This one is in the 29th percentile – i.e., 29% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 265,842 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 27th percentile – i.e., 27% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 46 others from the same source and published within six weeks on either side of this one. This one is in the 30th percentile – i.e., 30% of its contemporaries scored the same or lower than it.