Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1

Dóra Tombácz; Gábor Torma; Gábor Gulyás; Ádám Fülöp; Ákos Dörmő; István Prazsák; Zsolt Csabai; Máté Mizik; Ákos Hornyák; Zoltán Zádori; Balázs Kakuk; Zsolt Boldogkői

doi:10.1016/j.heliyon.2023.e17716

Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1

Heliyon. 2023 Jun 28;9(7):e17716. doi: 10.1016/j.heliyon.2023.e17716. eCollection 2023 Jul.

Affiliations

¹ Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary.
² Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary.

Abstract

This study employed both short-read sequencing (SRS, Illumina) and long-read sequencing (LRS Oxford Nanopore Technologies) platforms to conduct a comprehensive analysis of the equid alphaherpesvirus 1 (EHV-1) transcriptome. The study involved the annotation of canonical mRNAs and their transcript variants, encompassing transcription start site (TSS) and transcription end site (TES) isoforms, in addition to alternative splicing forms. Furthermore, the study revealed the presence of numerous non-coding RNA (ncRNA) molecules, including intergenic and antisense transcripts, produced by EHV-1. An intriguing finding was the abundant production of chimeric transcripts, some of which potentially encode fusion polypeptides. Moreover, EHV-1 exhibited a greater incidence of transcriptional overlaps and splicing compared to related viruses. It is noteworthy that many genes have their unique TESs along with the co-terminal transcription ends, a characteristic scarcely seen in other alphaherpesviruses. The study also identified transcripts that overlap the replication origins of the virus. Moreover, a novel ncRNA, referred to as NOIR, was found to intersect with the 5'-ends of longer transcript isoform specified by the major transactivator genes ORF64 and ORF65, surrounding the OriL. These findings together imply the existence of a key regulatory mechanism that governs both transcription and replication through, among others, a process that involves interference between the DNA and RNA synthesis machineries.

Keywords: Direct RNA sequencing; EHV-1; Equid alphaherpesvirus 1; Illumina sequencing; Long-read sequencing; Nanopore sequencing; Replication origin; Transcriptome.