Author Correction: Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist.

Funder: Canadian Institutes of Health Research (Grant: FRN-142349) Natural Sciences and Engineering Research Council of Canada (Grant: RGPIN 05871-2014)Abstract: Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes

Génomique des virus géants, des virophages, et échanges génétiques avec leurs hôtes eucaryotes

Nucleo Cytoplasmic Large DNA Viruses (NCLDV) form a very diverse group of double-stranded DNA viruses exclusively infecting eukaryotes. The NCLDVs contain the so-called "giant" viruses visible under light microscope, the first specimen of which, discovered in 2003, opened an unexplored field of viral biodiversity. Some families of NCLDVs could be as old as the emergence of contemporary cellular domains. These viruses inhabit a wide variety of environments (soils, oceans, etc.) where they contribute to the control of eukaryotic microbial populations (e.g., protists, phytoplankton). Moreover, some of these viruses are parasitized by smaller viruses, the virophages, that use the giant virus machinery for their own replication in a common cellular host. Understanding NCLDVs’ evolution, biodiversity and host / virus/virophage interactions is now one of the major areas of virology. Using genomics and bioinformatics approaches, I pursued two objectives in this thesis: (1) Characterize the biodiversity and evolution within the taxonomic family of Mimiviridae (NCLDV) through the description and comparative analysis of the genome of the virus "CeV" which infects the unicellular alga haptophyte Haptolina (ex Chrysochromulina) ericina; (2) Characterize the co-evolution of NCLDVs and virophages with their eukaryotic hosts. This second part was addressed by studying horizontal transfers of viral DNA in the available sequences of eukaryotic genomes. The icosahedral particle of the CeV virus has a diameter of 160 nm and contains a 474-kb genome. The analysis of the latter confirmed that CeV is related to the viruses of the Mimiviridae family, originally defined around the giant viruses prototypes Mimivirus and Megavirus which infect the amoebae. Other members of the Mimiviridae, closer to CeV, also infect unicellular algae. Together with CeV, the latter form a subgroup that we proposed to cluster into the subfamily Mesomimivirinae. Mesomimivirinae possess exclusive genomic characters: a second copy of the RNA polymerase gene, the presence of a gene coding for a second capsid protein, and 7 other groups of orthologous genes absent in other Mimiviridae. Despite their relatedness, each of these viruses possesses a majority of unique genes, the origin of which is unknown. On the other hand, several cases of parallel acquisitions by horizontal transfer of the same gene by CeV and other unrelated viruses were analyzed. This manuscript also documents genetic events that have occurred only in CeV, such as unique gene fusions. Bioinformatic screening of the sequence databases revealed DNA fragments of varying sizes (up to ~ 500Kb) integrated into the genomes of many eukaryotes, originally belonging to NCLDVs or virophages. Their analysis allowed to widen the spectrum of known NCLDVs’ hosts and suggest the existence of new viral families that remain to be discovered. Also, these inserts contain genes that are not found in the sequenced NCLDVs genomes, and could encode novel functionalities of the donor virus. Copies of virophage genomes integrated into the Bigelowiella natans algae genome suggest a new strategy for co-infection and dissemination of virophage, which may also constitute a defense mechanism against NCLDVs for the eukaryotic host.Les Nucleo Cytoplasmic Large DNA virus (NCLDV) forment un groupe très divers de virus à ADN double brin infectant exclusivement des eucaryotes. Les NCLDVs contiennent les-dits virus « géants » visibles au microscope optique, dont le premier spécimen découvert en 2003 a ouvert un champ inexploré de la biodiversité virale. Certaines familles de NCLDVs pourraient être aussi anciennes que l’émergence des domaines cellulaires contemporains. Ces virus habitent une grande variété d’environnements (sols, océans, etc.) dans lesquels ils concourent au contrôle des populations microbiennes eucaryotes (e.g., protistes, phytoplancton). Par ailleurs, certains de ces virus sont parasités par d’autres virus de taille plus modeste, les virophages. Ces derniers utilisent la machinerie de réplication des virus géants pour leur propre réplication dans un hôte cellulaire commun. La compréhension de l’évolution, la biodiversité et des interactions hôte/virus/virophage chez les NCLDVs est aujourd’hui un des grands chantiers de la virologie.A l’aide d’approches génomiques et bioinformatiques, deux objectifs ont été poursuivis dans ce travail de thèse: (1) Caractériser la biodiversité et l’évolution au sein de la famille taxonomique des Mimiviridae (NCLDV) à travers la description et l’analyse comparative du génome du virus « CeV » qui infecte l’algue unicellulaire haptophyte Haptolina (ex Chrysochromulina) ericina; (2) Caractériser la co-évolution des NCLDVs et des virophages avec leurs hôtes eucaryotes. Ce deuxième volet a été adressé en étudiant les transferts horizontaux d’ADNs viraux dans les génomes eucaryotes séquencés.La particule icosahédrique du virus CeV a un diamètre de 160 nm et contient un génome de 474-kb dont l’analyse a confirmé que CeV est apparenté aux virus de la famille des Mimiviridae, initialement définie autour des virus géant prototypes Mimivirus et Megavirus infectant des amibes. D’autres membres des Mimiviridae, plus proches de CeV, infectent aussi des espèces d’algues unicellulaires. Ces derniers forment un sous-groupe, que nous proposons d’élever au rang d’une sous-famille, les Mesomimivirinae. Les Mesomimivirinae possèdent des caractères génomiques exclusifs: une deuxième copie du gène de l’ARN polymérase, la présence d’un gène codant pour seconde protéine de capside, ainsi que 7 autres groupes de gènes orthologues absents chez les autres Mimiviridae. En dépit de leurs liens de parenté, chacun de ces virus possède une majorité de gènes qui lui est unique, et dont l’origine est inconnue. D’autre part, plusieurs cas indépendants d’acquisition par transfert horizontal du même gène par CeV et d’autres virus non-apparentés ont été analysés. Cette thèse documente également des évènements génétiques qui se sont produits dans la seule lignée de CeV, comme par exemple des fusions de gènes inédites.Le criblage bioinformatique des bases de données de séquences a mis en évidence des fragments d’ADNs de tailles variables (jusqu’à ~500Kb) intégrés au sein des génomes de nombreux eucaryotes, ayant originellement appartenus à des NCLDVs ou des virophages. Leur analyse a permis d’élargir le spectre d’hôtes connus des NCLDVs et suggèrent l’existence de nouvelles familles virales qui restent à découvrir. Egalement, ces insertions contiennent des gènes que l’on ne retrouve pas dans les génomes de NCLDVs séquencés, et pourraient coder pour des fonctionnalités inédites du virus donneur. Des copies de génomes de virophages intégrées au génome de l’algue Bigelowiella natans suggèrent une nouvelle stratégie de co-infection et de dissémination du virophage, qui pourrait aussi constituer un mécanisme de défense contre les NCLDVs pour l’hôte eucaryote

A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window

The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases. A total of 66 eukaryotic genomic or transcriptomic datasets—many of which are from algae and aquatic protists—contained at least one of the five most consistently conserved NCLDV core genes. Phylogenetic study of the eukaryotic NCLDV-like sequences identified putative new members of already recognized viral families, as well as members of as yet unknown viral clades. Genomic evidence suggested that most of these sequences resulted from viral DNA integrations rather than contaminating viruses. Furthermore, the nature of the inserted viral genes helped predicting original functional capacities of the donor viruses. These insights confirm that genomic insertions of NCLDV DNA are common in eukaryotes and can be exploited to delineate the contours of NCLDV biodiversity

A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window

International audienceThe nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases. A total of 66 eukaryotic genomic or transcriptomic datasets—many of which are from algae and aquatic protists—contained at least one of the five most consistently conserved NCLDV core genes. Phylogenetic study of the eukaryotic NCLDV-like sequences identified putative new members of already recognized viral families, as well as members of as yet unknown viral clades. Genomic evidence suggested that most of these sequences resulted from viral DNA integrations rather than contaminating viruses. Furthermore, the nature of the inserted viral genes helped predicting original functional capacities of the donor viruses. These insights confirm that genomic insertions of NCLDV DNA are common in eukaryotes and can be exploited to delineate the contours of NCLDV biodiversity

Comparative Genomics of Chrysochromulina Ericina Virus and Other Microalga-Infecting Large DNA Viruses Highlights Their Intricate Evolutionary Relationship with the Established Mimiviridae Family

International audienceChrysochromulina Ericina Virus CeV-01B was isolated from Norwegian coastal waters in 1998. Its icosahedral particle is 160 nm in diameter and encloses a 474-kb dsDNA genome. This virus, although infecting a microalgae (the haptophycea Haptolina ericina, formerly Chrysochromulina ericina), is phylogenetically related to members of the Mimiviridae family, initially established with the acanthamoeba-infecting Mimivirus and Megavirus as prototypes. This family was latter split into two genera (Mimivirus and Cafetariavirus) following the characterization of a virus infecting the heterotrophic stramenopile Cafeteria roenbergensis (CroV). CeV, as well as two of its close relatives infecting the unicellular photosynthetic eukaryotes Phaeocystis globosa (PgV) and Aureococcus anophagefferens (AaV), are currently unclassified by ICTV. The detailed comparative analysis of the CeV genome presented here confirms the phylogenetic affinity of this emerging group of microalgae-infecting viruses with the Mimiviridae, but argue in favor of their classification inside a distinct clade within the family. Although CeV, PgV, AaV share more common features between them than with the larger Mimiviridae, they also exhibit a large complement of unique genes attesting of their complex evolutionary history. We identified several gene fusion events and cases of convergent evolution involving independent lateral gene acquisitions. Finally, CeV possesses an unusual number of inteins, some of which are closely related despite been inserted in non-homologous genes. This appears to contradict the paradigm of allele-specific inteins and suggests that Mimiviridae might be especially efficient in spreading inteins while enlarging their repertoire of homing genes

The 474-Kilobase-Pair Complete Genome Sequence of CeV-01B, a Virus Infecting Haptolina (Chrysochromulina) ericina(Prymnesiophyceae)

We report the complete genome sequence of CeV-01B, a large double-stranded DNA virus infecting the unicellular marine phytoplankton Haptolina (formerly Chrysochromulina) ericina. CeV-01B and its closest relative Phaeocystis globosa virus define an emerging subclade of the Megaviridae family with smaller genomes and particles than the originally described giant Mimiviridae infecting Acanthamoeba

The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses

Viruses are the most abundant biological entities in the world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these are the recently described mirusviruses, which share some similarities with herpesviruses.1 50 years ago, "herpes-type" viral particles2 were found in a thraustochytrid member of the labyrinthulomycetes, a diverse group of abundant and ecologically important marine eukaryotes,3,4 but could not be further characterized by methods then available. Long-read sequencing has allowed us to connect the biology of mirusviruses and thraustochytrids. We sequenced the genome of the genetically tractable model thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381 and found that its 26 linear chromosomes have an extraordinary configuration. Subtelomeric ribosomal DNAs (rDNAs) found at all chromosome ends are interspersed with long repeated sequence elements denoted as long repeated-telomere and rDNA spacers (LORE-TEARS). We identified two genomic elements that are related to mirusvirus genomes. The first is a ∼300-kbp episome (circular element 1 [CE1]) present at a high copy number. Strikingly, the second, distinct, mirusvirus-like element is integrated between two sets of rDNAs and LORE-TEARS at the left end of chromosome 15 (LE-Chr15). Similar to metagenomically derived mirusviruses, these putative A. limacinum mirusviruses have a virion module related to that of herpesviruses along with an informational module related to nucleocytoplasmic large DNA viruses (NCLDVs). CE1 and LE-Chr15 bear striking similarities to episomal and endogenous latent forms of herpesviruses, respectively, and open new avenues of research into marine virus-host interactions