title: Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses.
abstract: BACKGROUND
  Giant viruses in the genus Chlorovirus (family Phycodnaviridae) infect eukaryotic green microalgae. The prototype member of the genus, Paramecium bursaria chlorella virus 1, was sequenced more than 15 years ago, and to date there are only 6 fully sequenced chloroviruses in public databases. Presented here are the draft genome sequences of 35 additional chloroviruses (287 - 348 Kb/319 - 381 predicted protein encoding genes) collected across the globe; they infect one of three different green algal species. These new data allowed us to analyze the genomic landscape of 41 chloroviruses, which revealed some remarkable features about these viruses.
  
  
  RESULTS
  Genome colinearity, nucleotide conservation and phylogenetic affinity were limited to chloroviruses infecting the same host, confirming the validity of the three previously known subgenera. Clues for the existence of a fourth new subgenus indicate that the boundaries of chlorovirus diversity are not completely determined. Comparison of the chlorovirus phylogeny with that of the algal hosts indicates that chloroviruses have changed hosts in their evolutionary history. Reconstruction of the ancestral genome suggests that the last common chlorovirus ancestor had a slightly more diverse protein repertoire than modern chloroviruses. However, more than half of the defined chlorovirus gene families have a potential recent origin (after Chlorovirus divergence), among which a portion shows compositional evidence for horizontal gene transfer. Only a few of the putative acquired proteins had close homologs in databases raising the question of the true donor organism(s). Phylogenomic analysis identified only seven proteins whose genes were potentially exchanged between the algal host and the chloroviruses.
  
  
  CONCLUSIONS
  The present evaluation of the genomic evolution pattern suggests that chloroviruses differ from that described in the related Poxviridae and Mimiviridae. Our study shows that the fixation of algal host genes has been anecdotal in the evolutionary history of chloroviruses. We finally discuss the incongruence between compositional evidence of horizontal gene transfer and lack of close relative sequences in the databases, which suggests that the recently acquired genes originate from a still largely un-sequenced reservoir of genomes, possibly other unknown viruses that infect the same hosts.
authors.affiliation: Information Génomique & Structurale, IGS UMR7256, CNRS, Aix-Marseille Université, FR-13288, Marseille, France.
authors.forename: Adrien
authors.initials: A
authors.lastname: Jeanniard
authors.forename: David D
authors.initials: DD
authors.lastname: Dunigan
authors.forename: James R
authors.initials: JR
authors.lastname: Gurnon
authors.forename: Irina V
authors.initials: IV
authors.lastname: Agarkova
authors.forename: Ming
authors.initials: M
authors.lastname: Kang
authors.forename: Jason
authors.initials: J
authors.lastname: Vitek
authors.forename: Garry
authors.initials: G
authors.lastname: Duncan
authors.forename: O William
authors.initials: OW
authors.lastname: McClung
authors.forename: Megan
authors.initials: M
authors.lastname: Larsen
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Claverie
authors.forename: James L
authors.initials: JL
authors.lastname: Van Etten
authors.forename: Guillaume
authors.initials: G
authors.lastname: Blanc
mesh_terms: D005075:Biological Evolution; D000460:Chlorophyta / Q000235:genetics* / Q000821:virology; D004267:DNA Viruses / Q000145:classification / Q000235:genetics*; D022761:Gene Transfer, Horizontal; D016679:Genome, Viral; D017862:Phycodnaviridae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D014764:Viral Proteins
chemical_list: D014764:Viral Proteins