Faustovirus E12 Transcriptome Analysis Reveals Complex Splicing in Capsid Gene.

Faustoviruses are the first giant viruses of amoebae isolated on . 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 ( = 5) and spliceosome-like introns with non-canonical splice sites ( = 7). All splice-sites were non-canonical with five types of donor/acceptor splice-sites among which AA/TG was the most frequent association.