title: Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells.
abstract: Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating co-assembly that features >74% of genome recovery, against about 20% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questions.
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Mangot
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain.
authors.forename: Ramiro
authors.initials: R
authors.lastname: Logares
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Sánchez
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain.
authors.forename: Fran
authors.initials: F
authors.lastname: Latorre
authors.affiliation: CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, Evry F-91000, France.|CNRS, UMR 8030, CP5706, Evry, F-91000, France.|Université d'Evry, UMR 8030, CP5706, Evry, F-91000, France.
authors.forename: Yoann
authors.initials: Y
authors.lastname: Seeleuthner
authors.affiliation: CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, Evry F-91000, France.|CNRS, UMR 8030, CP5706, Evry, F-91000, France.|Université d'Evry, UMR 8030, CP5706, Evry, F-91000, France.
authors.forename: Samuel
authors.initials: S
authors.lastname: Mondy
authors.affiliation: National Science Foundation, 4201 Wilson Boulevard, Arlington, VA 22230, USA.|Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME 04544, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Sieracki
authors.affiliation: CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, Evry F-91000, France.|CNRS, UMR 8030, CP5706, Evry, F-91000, France.|Université d'Evry, UMR 8030, CP5706, Evry, F-91000, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Jaillon
authors.affiliation: CEA, Institut de Génomique, Génoscope, 2 Rue Gaston Crémieux, Evry F-91000, France.|CNRS, UMR 8030, CP5706, Evry, F-91000, France.|Université d'Evry, UMR 8030, CP5706, Evry, F-91000, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France.|Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, F-29680, France.
authors.forename: Colomban de
authors.initials: C
authors.lastname: Vargas
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain.
authors.forename: Ramon
authors.initials: R
authors.lastname: Massana
mesh_terms: D059001:Aquatic Organisms / Q000235:genetics; D001483:Base Sequence; D056890:Eukaryota / Q000235:genetics*; D016678:Genome; D023281:Genomics; D009792:Oceans and Seas; D010802:Phylogeny; D012270:Ribosomes / Q000378:metabolism; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis