title: Characterization of pseudorabies virus transcriptome by Illumina sequencing.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary. olah.peter@med.u-szeged.hu.
authors.forename: Péter
authors.initials: P
authors.lastname: Oláh
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary. tombacz.dora@med.u-szeged.hu.
authors.forename: Dóra
authors.initials: D
authors.lastname: Tombácz
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary. poka.nandor@med.u-szeged.hu.
authors.forename: Nándor
authors.initials: N
authors.lastname: Póka
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary. csabai.zsolt@med.u-szeged.hu.
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Csabai
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary. prazsak.istvan@med.u-szeged.hu.
authors.forename: István
authors.initials: I
authors.lastname: Prazsák
authors.affiliation: Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary. boldogkoi.zsolt@med.u-szeged.hu.
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Boldogkői
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D016679:Genome, Viral; D011558:Herpesvirus 1, Suid / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008969:Molecular Sequence Data; D026723:Polyadenylation; D022821:RNA Splice Sites; D012333:RNA, Messenger / Q000032:analysis; D012367:RNA, Viral / Q000032:analysis; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D022821:RNA Splice Sites; D012333:RNA, Messenger; D012367:RNA, Viral