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A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window.
Viruses. 2017 01 20; 9(1)V

Abstract

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.

Authors+Show Affiliations

Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS UMR7256 (IMM FR3479), 13288 Marseille cedex 09, France. lucie.gallot-lavallee@igs.cnrs-mrs.fr.Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS UMR7256 (IMM FR3479), 13288 Marseille cedex 09, France. guillaume.blanc@igs.cnrs-mrs.fr. Mediterranean Institute of Oceanography (MIO), Aix Marseille Université, Université de Toulon, CNRS/INSU, IRD, UM 110, 13288 Marseille cedex 09, France. guillaume.blanc@igs.cnrs-mrs.fr.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28117696

Citation

Gallot-Lavallée, Lucie, and Guillaume Blanc. "A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity Through the Eukaryotic Genomics Window." Viruses, vol. 9, no. 1, 2017.
Gallot-Lavallée L, Blanc G. A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window. Viruses. 2017;9(1).
Gallot-Lavallée, L., & Blanc, G. (2017). A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window. Viruses, 9(1). https://doi.org/10.3390/v9010017
Gallot-Lavallée L, Blanc G. A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity Through the Eukaryotic Genomics Window. Viruses. 2017 01 20;9(1) PubMed PMID: 28117696.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window. AU - Gallot-Lavallée,Lucie, AU - Blanc,Guillaume, Y1 - 2017/01/20/ PY - 2016/11/30/received PY - 2017/01/13/revised PY - 2017/01/13/accepted PY - 2017/1/25/entrez PY - 2017/1/25/pubmed PY - 2017/9/28/medline KW - lateral gene transfer KW - nucleo-cytoplasmic large DNA virus KW - virus insertion JF - Viruses JO - Viruses VL - 9 IS - 1 N2 - 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. SN - 1999-4915 UR - https://www.unboundmedicine.com/medline/citation/28117696/A_Glimpse_of_Nucleo_Cytoplasmic_Large_DNA_Virus_Biodiversity_through_the_Eukaryotic_Genomics_Window_ L2 - https://www.mdpi.com/resolver?pii=v9010017 DB - PRIME DP - Unbound Medicine ER -
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