Abstract
With genomes of up to 2.7 Mb propagated in micrometer-long oblong particles and initially predicted to encode more than 2000 proteins, members of the Pandoraviridae family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution. A previous analysis of six newly available isolates, independently confirmed by a study including 3 others, established that the Pandoraviridae pan-genome is open, meaning that each new strain exhibits protein-coding genes not previously identified in other family members. With an average increment of about 60 proteins, the gene repertoire shows no sign of reaching a limit and remains largely coding for proteins without recognizable homologs in other viruses or cells (ORFans). To explain these results, we proposed that most new protein-coding genes were created de novo, from pre-existing non-coding regions of the G+C rich pandoravirus genomes. The comparison of the gene content of a new isolate, P. celtis, closely related (96 % identical genome) to the previously described P. quercus is now used to test this hypothesis by studying genomic changes in a microevolution range. Our results confirm that the differences between these two similar gene contents mostly consist of protein-coding genes without known homologs (ORFans), with statistical signatures close to that of intergenic regions. These newborn proteins are under slight negative selection, perhaps to maintain stable folds and prevent protein aggregation pending the eventual emergence of fitness-increasing functions. Our study also unraveled several insertion events mediated by a transposase of the hAT family, 3 copies of which are found in P. celtis and are presumably active. Members of the Pandoraviridae are presently the first viruses known to encode this type of transposase.
Footnotes
In this revised version, we provide a list of the P. celtis ncRNAs as supplementary Table S1. We also performed a complete comparison of these ncRNAs with those of P. quercus, and analyzed their correlation with de novo created proteins. These new results are now presented in a specific section (3.5), and further discussed in the discussion (line 390-392). This additional work allowed us to refine our proposed evolutionary model, now suggesting that ORFs are opening first, before eventually becoming transcribed. We also performed some polishing of the P. celtis genome sequence. This revealed a few errors that have now been corrected in a revised Genbank entry (same accession number). These corrections only changed the annotation of a handful of genes, that have been corrected, such as in Table 1 (3 P. celtis candidate new genes are no longer predicted: cds_649, cds_898, cds 764).
