Acanthamoeba polyphaga de novo transcriptome and its dynamics during Mimivirus infection

Acanthamoeba polyphaga mimivirus (Mimivirus) is a giant virus that infects Acanthamoeba species – opportunistic human pathogens. We applied long- and short-read sequencing to generate a de novo transcriptome of the host and followed the dynamics of both host and virus transcriptomes over the course of infection. The assembled transcriptome of the host included 22,604 transcripts and 13,043 genes, with N50 = 2,372 nucleotides. Functional enrichment analysis revealed major changes in the host transcriptome, namely, enrichment in downregulated genes associated with cytoskeleton homeostasis and DNA replication, repair, and nucleotide synthesis. These modulations, together with those implicated by other enriched processes, indicate cell cycle arrest, an event we demonstrated experimentally. We also observed upregulation of host genes associated with transcription, secretory pathways and, as reported here for the first time, peroxisomes and the ubiquitin-proteasome system. In Mimivirus, the early stages of infections were marked by upregulated genes related to DNA replication, transcription, translation, and nucleotide metabolism, and the later stages, by enrichment in genes associated with lipids metabolism, carbohydrates, and proteases. Some of the changes observed in the amoebal transcriptome likely point to Mimivirus infection causing the dismantling of the host cytoskeleton, the translocation of endoplasmic reticulum membranes to viral factory areas, and cell cycle arrest. ### Competing Interest Statement The authors have declared no competing interest. * AC : Acanthamoeba castellanii AP : Acanthamoeba polyphaga bp : base pairs BUSCO : Benchmarking Universal Single-Copy Ortholog DEGs : differentially expressed genes DR : downregulated ER : endoplasmic reticulum ERAD : ER- associated degradation FDR : false discovery rate GO : Gene Ontology HIV : human immunodeficiency virus HPV : human papilloma virus CMV : cytomegalovirus LR : long read NCLDV : nucleo-cytoplasmatic large DNA virus NGS : next-generation sequencing NLR : NOD-like receptors ORF : open reading frame PCA : principal component analysis HPI : hours post infection RT : room temperature SMRT : single-molecule, real-time SR : short reads TF : transcription factor URG : upregulated genes VF : viral factory VV : vaccinia virus