Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses

Authors

Adrien Jeanniard, Aix-Marseille Université
David D. Dunigan, University of Nebraska-LincolnFollow
James Gurnon, University of Nebraska-LincolnFollow
Irina V. Agarkova, University of Nebraska-LincolnFollow
Ming Kang, University of Nebraska-LincolnFollow
Jason Vitek, University of Nebraska-Lincoln
Garry Duncan, Nebraska Wesleyan UniversityFollow
O William McClung, Nebraska Wesleyan University
Megan Larsen, Indiana University - Bloomington
Jean-Michel Claverie, University of Nebraska-Lincoln
James L. Van Etten, University of Nebraska-LincolnFollow
Guillaume Blanc, University of Nebraska-Lincoln

ORCID IDs

David D. Dunigan

Irina V. Agarkova

James L. Van Etten

Document Type

Article

Date of this Version

2013

Citation

Jeanniard, Dunigan, Gurnon, Agarkova, Kang, Vitek, Duncan, McClung, Larsen, Claverie, Van Etten & Blanc in BMC Genomics (2013) 14. DOI:10.1186/1471-2164-14-158

Comments

Copyright 2013, the authors. Used by permission.

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.

Conclusion: 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.