Viral evolution

A phylogenomic data-driven exploration of viral origins and evolution

“…7A ). Some giant viruses appeared more derived, supporting their ancient coexistence with cells ( 19 , 73 ). The topology and ordering of proteomes in evoPCO analysis were further supported by a distance-based neighbor-joining (NJ) tree ( Fig.…”

Do Viruses Exchange Genes across Superkingdoms of Life?

“…First, the detection of ABE FSFs in viral proteomes effectively transforms ABE into an ABEV group, which now represents a large core of (near)-universal FSF domains shared by both cells and viruses. The mere existence of this FSF core supports an early “cell-like” phase in the evolution of modern viruses, an idea that has recently become popular (Nasir et al, 2012a , b ) following the discovery of several “giant viruses” that overlap parasitic cells in physical and genome size (La Scola et al, 2003 ; Philippe et al, 2013 ; Legendre et al, 2014 , 2015 ). Under this proposal, viruses are secondarily acellular as they either “escaped” or “reduced” from primordial cells before these cells diversified into superkingdoms (Nasir and Caetano-Anollés, 2015 , see Schulz et al, 2017 for an opposite view).…”

“…This method reliably detects HGT events (Philippe and Douady, 2003 ), especially in viral genes where sequence identity with cellular counterparts may be too low to produce meaningful alignment-dependent phylogenetic trees (Nasir and Caetano-Anollés, 2015 ). The tracings yielded unique insights into genetic transfers between viruses and cells, highlighted the quantitatively greater cross-superkingdom genetic exchange occurring between bacterioviruses and eukaryotes and eukaryoviruses and bacteria, and supported models of viral origins from ancient cells (Nasir et al, 2012b ). The genetic crosstalk between viral and cellular proteomes that we uncover with this comparative genomics approach presents a more global picture for evolutionary understanding of virus-cell interactions that goes beyond the perceived textbook definitions of virus hosts (Nasir et al, 2017 ).…”

“…In turn, if an FSF involved in cellular hallmark function (e.g., metabolism) and widespread in cellular proteomes (e.g., >60% presence) was detected in some viral proteomes then this was FSF was determined to have transferred horizontally from cell to viruses. The exception would be the presence of “cell-like” FSFs in the proteomes of all three virus groups, i.e., archaeoviruses, bacterioviruses , and eukaryoviruses , suggesting a cellular co-existence between viral and cellular ancestors prior to diversification of modern life (Nasir et al, 2012a , b ). Thus, both the FSF spread and its biochemical function were considered when postulating the direction of gene transfer.…”

“…Similarly, eukaryoviruses often capture genes involved in antiviral immunity from eukaryotic cells (Elde and Malik, 2009 ; Rappoport and Linial, 2012 ). Thus, host-constrained evolution of viral lineages has led to favoring either the “escape” or “reduction” models for the origin of modern viruses, both attributing viral origins from modern or ancient host cells (reviewed in Hendrix et al, 2000 ; Forterre and Krupovic, 2012 ; Nasir et al, 2012b ).…”