Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes. Benites, L. F., Poulton, N., Labadie, K., Sieracki, M. E., Grimsley, N., & Piganeau, G. Philos Trans R Soc Lond B Biol Sci, 374(1786):20190089, 2019.
Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes [link]Paper  doi  abstract   bibtex   
Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 microm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13-22 Mb genomes from three genera, Ostreococcus, Bathycoccus and 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 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 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'.
@article{RN136,
   author = {Benites, L. F. and Poulton, N. and Labadie, K. and Sieracki, M. E. and Grimsley, N. and Piganeau, G.},
   title = {Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes},
   journal = {Philos Trans R Soc Lond B Biol Sci},
   volume = {374},
   number = {1786},
   pages = {20190089},
   abstract = {Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 microm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13-22 Mb genomes from three genera, Ostreococcus, Bathycoccus and 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 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 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'.},
   keywords = {Chlorophyta/genetics/*physiology/virology
DNA Viruses/*physiology
*Genome
*Tara-Oceans
*cross-contamination
*mating type
*picoeukaryotes
*single amplified genome
*virus},
   ISSN = {1471-2970 (Electronic)
0962-8436 (Linking)},
   DOI = {10.1098/rstb.2019.0089},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/31587637},
   year = {2019},
   type = {Journal Article}
}

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