Anguillid herpesvirus 1 transcriptomics

We used deep sequencing of poly(A) RNA to characterize the transcriptome of an economically important eel herpesvirus, anguillid herpesvirus 1 (AngHV1), at a stage during the lytic life cycle when infectious virus was being produced. In contrast to mammalian herpesviruses, the overall level of antisense transcription from the 248526 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 10634 bp terminal direct repeat once, 100 splice junctions were identified, of which 58 were inferred to be the most likely to be functional 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 the 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 of these and adding others by RACE. The findings prompted a revision of the AngHV1 genome map to include a total of 129 protein-coding genes, five of which are duplicated in the terminal direct repeat. Eleven genes contain integral, spliced protein-coding exons, and nine 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.