Third-generation Sequencing Reveals Extensive Polycistronism and Transcriptional Overlapping in a Baculovirus

The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is an insect-pathogen baculovirus. In this study, we applied the Oxford Nanopore Technologies platform for the analysis of the polyadenylated fraction of the viral transcriptome using both cDNA and direct RNA sequencing methods. We id...

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Bibliographic Details
Published in:Scientific reports 2018-06, Vol.8 (1), p.8604-11, Article 8604
Main Authors: Moldován, Norbert, Tombácz, Dóra, Szűcs, Attila, Csabai, Zsolt, Balázs, Zsolt, Kis, Emese, Molnár, Judit, Boldogkői, Zsolt
Format: Article
Language:English
Subjects:
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Bioinformatics
Gene expression
Gene Expression Profiling
Genes
Genes, Viral
Genomes
High-Throughput Nucleotide Sequencing
Humanities and Social Sciences
Infections
Isoforms
Molecular Sequence Annotation
multidisciplinary
Non-coding RNA
Nucleopolyhedroviruses - genetics
Polyadenylation
Proteins
RNA polymerase
Science
Science (multidisciplinary)
Transcription
Transcription Initiation Site
Transcription, Genetic
Viral infections
Viruses
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Summary:The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is an insect-pathogen baculovirus. In this study, we applied the Oxford Nanopore Technologies platform for the analysis of the polyadenylated fraction of the viral transcriptome using both cDNA and direct RNA sequencing methods. We identified and annotated altogether 132 novel transcripts and transcript isoforms, including 4 coding and 4 non-coding RNA molecules, 47 length variants, 5 splice isoforms, as well as 23 polycistronic and 49 complex transcripts. All of the identified novel protein-coding genes were 5′-truncated forms of longer host genes. In this work, we demonstrated that in the case of transcript start site isoforms, the promoters and the initiator sequence of the longer and shorter variants belong to the same kinetic class. Long-read sequencing also revealed a complex meshwork of transcriptional overlaps, the function of which needs to be clarified. Additionally, we developed bioinformatics methods to improve the transcript annotation and to eliminate the non-specific transcription reads generated by template switching and false priming.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-018-26955-8