title: Identification of a Marine Cyanophage in a Protist Single-cell Metagenome Assembly.
abstract: Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P. chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P. chromatophora that are related to P. ovalis and found one SCG assembly to contain α-cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200 Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.
authors.affiliation: Department of Ecology, Evolution and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, 08901, USA.
authors.forename: Debashish
authors.initials: D
authors.lastname: Bhattacharya
authors.affiliation: Department of Ecology, Evolution and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, 08901, USA.
authors.forename: Dana C
authors.initials: DC
authors.lastname: Price
authors.affiliation: Unité Mixte de Recherche, Centre National de la Recherche Scientifique 7138, Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Paris, 75005, France.
authors.forename: Cedric
authors.initials: C
authors.lastname: Bicep
authors.affiliation: Unité Mixte de Recherche, Centre National de la Recherche Scientifique 7138, Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Paris, 75005, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Bapteste
authors.affiliation: Department of Ecology, Evolution Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA.
authors.forename: Mihir
authors.initials: M
authors.lastname: Sarwade
authors.affiliation: Department of Ecology, Evolution Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA.
authors.forename: Veeran D
authors.initials: VD
authors.lastname: Rajah
authors.affiliation: Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, Korea.
authors.forename: Hwan Su
authors.initials: HS
authors.lastname: Yoon
keywords: Paulinella; cyanophage; gene network; horizontal gene transfer; phylogenomics; single cell genomics