Marine viruses-Major players in the global ecosystem, Nat. Rev. Microbiol, vol.5, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-01663342
High abundance of viruses found in aquatic environments, Nature, vol.340, pp.467-468, 1989. ,
Re-examination of the relationship between marine virus and microbial cell abundances, Nat. Microbiol, 2016. ,
Marine viruses and their biogeochemical and ecological effects, Nature, vol.399, pp.541-548, 1999. ,
Roles of viruses in the environment, Environ. Microbiol, vol.11, pp.2771-2774, 2009. ,
Marine viruses and global climate change, FEMS Microbiol. Rev, vol.35, pp.993-1034, 2011. ,
Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan, ISME J, vol.12, pp.1287-1295, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01771838
Plankton networks driving carbon export in the oligotrophic ocean, Nature, vol.532, pp.465-470, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01275276
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses, Nature, vol.537, pp.689-693, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01376822
Environmental viral genomes shed new light on virus-host interactions in the ocean, vol.2, pp.359-375, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01771841
Biogeography of viruses in the sea, Annu. Rev. Virol, vol.2, pp.41-66, 2015. ,
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes, ISME J, vol.7, pp.1678-1695, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01258223
A global ocean atlas of eukaryotic genes, Nat. Commun, vol.9, 2018. ,
URL : https://hal.archives-ouvertes.fr/cea-01874711
Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae, Proc. Natl. Acad. Sci, vol.108, pp.17486-17491, 2011. ,
Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes, Proc. Natl. Acad. Sci, vol.110, pp.10800-10805, 2013. ,
Taxon richness of "Megaviridae" exceeds those of Bacteria and Archaea in the ocean. Microbes Env, vol.33, pp.162-171, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01978927
Mimivirus and the emerging concept of "giant" virus, Virus Res, vol.117, pp.133-144, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00005228
Another really, really big virus, vol.3, pp.32-46, 2011. ,
Editorial introduction to "Giant Viruses" special issue of Virology, Virology, pp.466-467, 2014. ,
Comparative genomics of Chrysochromulina ericina virus and other microalga-infecting large DNA viruses highlights their intricate evolutionary relationship with the established Mimiviridae family, J. Virol, p.91, 2017. ,
The 1.2-Megabase genome sequence of Mimivirus, Science, vol.306, pp.1344-1350, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00651656
Giant virus with a remarkable complement of genes infects marine zooplankton, Proc. Natl. Acad. Sci, vol.107, pp.19508-19513, 2010. ,
Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host-virus coevolution, Virology, pp.466-467, 2014. ,
The 474-kilobase-pair complete genome sequence of CeV-01B, a virus infecting Haptolina (Chrysochromulina) ericina (Prymnesiophyceae), Genome Announc, vol.3, pp.1413-01415, 2015. ,
Megavirales", a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses, Arch. Virol, vol.158, pp.2517-2521, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01129809
Amplification of DNA polymerase gene fragments from viruses infecting microalgae, Appl. Environ. Microbiol, vol.61, pp.1274-1278, 1995. ,
Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes, Appl. Environ. Microbiol, vol.62, pp.2869-2874, 1996. ,
Phylogenetic analysis of members of the Phycodnaviridae virus family, using amplified fragments of the major capsid protein gene, Appl. Environ. Microbiol, vol.74, pp.3048-3057, 2008. ,
Seasonal dynamics of haptophytes and dsDNA algal viruses suggest complex virus-host relationship, vol.9, 2017. ,
DOI : 10.3390/v9040084
URL : https://www.mdpi.com/1999-4915/9/4/84/pdf
Development of DNA mismatch repair gene, MutS, as a diagnostic marker for detection and phylogenetic analysis of algal Megaviruses, Virology, pp.123-128, 2014. ,
Prasinovirus distribution in the Northwest Mediterranean Sea is affected by the environment and particularly by phosphate availability, Virology, pp.146-157, 2014. ,
Structure and function of the global ocean microbiome, Science, vol.348, p.1261359, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01233742
Application of the MAFFT sequence alignment program to large data-Reexamination of the usefulness of chained guide trees, Bioinformatics, vol.32, pp.3246-3251, 2016. ,
PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments, Nucleic Acids Res, vol.34, pp.609-612, 2006. ,
DOI : 10.1093/nar/gkl315
URL : https://academic.oup.com/nar/article-pdf/34/suppl_2/W609/7623711/gkl315.pdf
Profile hidden Markov models, Bioinformatics, vol.14, pp.755-763, 1998. ,
Tentative Characterization of new environmental giant viruses by MALDI-TOF mass spectrometry, Intervirology, vol.53, pp.344-353, 2010. ,
Linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree, BMC Bioinform, vol.11, 2010. ,
DOI : 10.1186/1471-2105-11-538
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-538
CD-HIT: Accelerated for clustering the next-generation sequencing data, Bioinformatics, vol.28, pp.3150-3152, 2012. ,
DOI : 10.1093/bioinformatics/bts565
URL : https://academic.oup.com/bioinformatics/article-pdf/28/23/3150/18529929/bts565.pdf
Fast gapped-read alignment with Bowtie 2, Nat. Methods, vol.9, pp.357-359, 2012. ,
DOI : 10.1038/nmeth.1923
URL : http://europepmc.org/articles/pmc3322381?pdf=render
Primer3-New capabilities and interfaces, Nucleic Acids Res, vol.40, 2012. ,
DOI : 10.1093/nar/gks596
URL : https://academic.oup.com/nar/article-pdf/40/15/e115/25343564/gks596.pdf
EMBOSS: The European Molecular Biology Open Software Suite, Trends Genet, vol.16, pp.276-277, 2000. ,
DOI : 10.1016/s0168-9525(00)02024-2
Diurnal infection patterns and impact of Microcystis cyanophages in a Japanese pond, Appl. Environ. Microbiol, vol.78, pp.5805-5811, 2012. ,
, Metagenomic Sequencing Library Preparation, p.13, 2018.
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet J, vol.17, pp.10-12, 2011. ,
DOI : 10.14806/ej.17.1.200
FLASH: Fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, pp.2957-2963, 2011. ,
Trimmomatic: A flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014. ,
DOI : 10.1093/bioinformatics/btu170
URL : https://academic.oup.com/bioinformatics/article-pdf/30/15/2114/17143152/btu170.pdf
UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.27, pp.2194-2200, 2011. ,
DOI : 10.1093/bioinformatics/btr381
URL : https://academic.oup.com/bioinformatics/article-pdf/27/16/2194/16901078/btr381.pdf
QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, vol.7, pp.335-336, 2010. ,
DOI : 10.1038/nmeth.f.303
URL : http://europepmc.org/articles/pmc3156573?pdf=render
, Freely available Python tools for computational molecular biology and bioinformatics, vol.25, pp.1422-1423, 2009.
DOI : 10.1093/bioinformatics/btp163
URL : https://academic.oup.com/bioinformatics/article-pdf/25/11/1422/944180/btp163.pdf
Basic local alignment search tool, J. Mol. Biol, vol.215, pp.403-410, 1990. ,
DOI : 10.1006/jmbi.1990.9999
Matplotlib: A 2D Graphics Environment, Comput. Sci. Eng, vol.9, pp.90-95, 2007. ,
DOI : 10.1109/mcse.2007.55
ETE 3: Reconstruction, analysis, and visualization of phylogenomic data, Mol.Biol. Evol, vol.33, pp.1635-1638, 2016. ,
DOI : 10.1093/molbev/msw046
URL : https://academic.oup.com/mbe/article-pdf/33/6/1635/7953632/msw046.pdf
The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea, vol.7, 2018. ,
Giant viruses with an expanded complement of translation system components, vol.356, pp.82-85, 2017. ,
DOI : 10.1126/science.aal4657
URL : http://science.sciencemag.org/content/356/6333/82.full.pdf
Marine mimivirus relatives are probably large algal viruses, Virol. J, vol.5, 2008. ,
DOI : 10.1186/1743-422x-5-12
URL : https://virologyj.biomedcentral.com/track/pdf/10.1186/1743-422X-5-12
Eukaryotic plankton diversity in the sunlit ocean, Science, vol.348, p.1261605, 2015. ,
Unveiling of the Diversity of Prasinoviruses (Phycodnaviridae) in Marine samples by using high-throughput sequencing analyses of PCR-amplified DNA polymerase and major capsid protein genes, Appl. Environ. Microbiol, vol.80, pp.3150-3160, 2014. ,
Diversity and dynamics of algal Megaviridae members during a harmful brown tide caused by the pelagophyte, Aureococcus anophagefferens, FEMS Microbiol. Ecol, vol.92, 2016. ,
Isolation and characterization of two viruses with large genome size infecting Chrysochromulina ericina (Prymnesiophyceae) and Pyramimonas orientalis (Prasinophyceae), Virology, vol.290, pp.272-280, 2001. ,
DOI : 10.1006/viro.2001.1161
URL : https://doi.org/10.1006/viro.2001.1161