Abstract
Faustoviruses are the first giant viruses of amoebae isolated on Vermamoeba vermiformis. They are distantly related to African swine fever virus, the causative agent of lethal hemorrhagic fever in domestic pigs. Structural studies have shown the presence of a double protein layer encapsidating the double-stranded DNA genome of Faustovirus E12, the prototype strain. The major capsid protein (MCP) forming the external layer has been shown to be 645-amino acid-long. Unexpectedly, its encoding sequence has been found to be scattered along a 17 kbp-large genomic region. Using RNA-seq, we studied expression of Faustovirus E12 genes at nine time points over its entire replicative cycle. Paired-end 250 bp-long read sequencing on MiSeq instrument and double-round spliced alignment enabled the identification of 26 different splice-junctions. Reads corresponding to junctions represented 2% of mapped reads and mostly matched with the predicted MCP encoding sequences. Moreover, our study enabled describing a 1,939 bp-long transcript that corresponds to the MCP, delineating 13 exons. At least two types of introns coexist in the MCP gene: group I introns that can self-splice (n = 5) and spliceosome-like introns with non-canonical splice sites (n = 7). All splice-sites were non-canonical with five types of donor/acceptor splice-sites among which AA/TG was the most frequent association.
Highlights
Faustoviruses are the first giant viruses of amoebae isolated using Vermamoeba vermiformis as cellular culture support (Reteno et al, 2015)
The transcriptome sequencing of Faustovirus E12-infected V. vermiformis resulted in 8,909,144 read pairs distributed over nine time points with two biological replicates corresponding to t = 0 min, 15 min, 90 min, 3 h, 6 h, and 8 h, and one replicate for t = 11, 17, and 20 h
We detected that Faustovirus E12 expresses during its replicative cycle 90% (445/492) of its predicted genes including all but two genes that were assigned an Nucleo-Cytoplasmic Virus Orthologous Groups (NCVOGs) ID (116/118) (Supplementary Table 1)
Summary
Faustoviruses are the first giant viruses of amoebae isolated using Vermamoeba vermiformis as cellular culture support (Reteno et al, 2015) Their capsids are icosahedral and virions are 200–240 nm large (Benamar et al, 2016). Four lineages could be inferred from phylogenetic analyses of the core genome, with no clustering of the strains according to their geographical origin (Benamar et al, 2016; Cherif Louazani et al, 2017) For all these isolates, many hypothetical proteins were predicted, for which no function could be inferred due to the absence of recognizable homologs or conserved domains, their number being 148 among proteins encoded by the core genes. We put a special focus on the identification of splicing events in the transcription process of the MCP encoding gene over the entire replicative cycle
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