Abstract
Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 µm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13-22 Mb genomes from three genera, $\textit{Ostreococcus}$, $\textit{Bathycoccus}$ and $\textit{Micromonas}$, are available from previously isolated clonal cultured strains and provide an ideal resource to explore the scope and challenges of analysing single cell amplified genomes (SAGs) isolated from a natural environment. We assembled data from 12 SAGs sampled during the Tara Oceans expedition to gain biological insights about their $\textit{in situ}$ ecology, which might be lost by isolation and strain culture. Although the assembled nuclear genomes were incomplete, they were large enough to infer the mating types of four $\textit{Ostreococcus}$ SAGs. The systematic occurrence of sequences from the mitochondria and chloroplast, representing less than 3% of the total cell's DNA, intimates that SAGs provide suitable substrates for detection of non-target sequences, such as those of virions. Analysis of the non-Mamiellophyceae assemblies, following filtering out cross-contaminations during the sequencing process, revealed two novel 1.6 and 1.8 kb circular DNA viruses, and the presence of specific Bacterial and Oomycete sequences suggests that these organisms might co-occur with the Mamiellales. This article is part of a discussion meeting issue 'Single cell ecology'.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 20190089 |
| Journal | Philosophical transactions of the Royal Society of London. Series B, Biological sciences |
| Volume | 374 |
| Issue number | 1786 |
| DOIs | |
| State | Published - Oct 8 2019 |
| Externally published | Yes |
Bibliographical note
KAUST Repository Item: Exported on 2021-09-09Acknowledgements: We thank Tom Delmont and Olivier Jaillon from the Genoscope for information about the SAGs, Lilian Caesar for help with the figures, and the Genotoul platform (www.genotoul.fr) for cluster availability for bioinformatics analysis and Genoscope for sequencing. We are grateful to Fabien Burki for making a perl script for extracting taxonomic affiliation from DIAMOND outputs available. Tara Oceans (which includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (http://oceans.taraexpeditions.org). We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, The French Ministry of Research and the French Government ‘Investissements d'Avenir’ programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL* Research University (ANR-11-IDEX-0001-02), Gordon and Betty Moore Foundation (award #3790) and the US National Science Foundation (awards OCE#1536989 and OCE#1829831) to M.E.S., as well as the Ohio Supercomputer for computational support. We are also grateful for the support and commitment of agnès b. and Etienne Bourgois, the Prince Albert II de Monaco Foundation, the Veolia Foundation, Region Bretagne, Lorient Agglomeration, Serge Ferrari, Worldcourier, and KAUST. The global sampling effort was enabled by countless scientists and crew who sampled aboard the Tara from 2009–2013, and we thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expeditions. We are also grateful to the countries that graciously granted sampling permissions. The authors declare that all data reported herein are fully and freely available from the date of publication, with no restrictions, and that all of the analyses, publications and ownership of data are free from legal entanglement or restriction by the various nations whose waters the Tara Oceans expeditions sampled in. The results and conclusions of this study do not represent the opinions or position of the U.S. National Science Foundation. This article is contribution number 91 of Tara Oceans. We also acknowledge three anonymous referees for constructive comments on a previous version of this manuscript
This publication acknowledges KAUST support, but has no KAUST affiliated authors.
ASJC Scopus subject areas
- General Agricultural and Biological Sciences
- General Biochemistry, Genetics and Molecular Biology
