Single cell genome analysis of an uncultured heterotrophic stramenopile

Roy, Raj; Price, Dana C.; Schliep, Alexander; Cai, Guohong; Korobeynikov, Anton; Yoon, Hwan Su; Yang, Eun Chan; Bhattacharya, Debashish

doi:10.1038/srep04780

Cited by 43 publications

(51 citation statements)

References 53 publications

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“…To overcome this limitation, Single Cells Genomics is a very promising approach2829. However, this approach has been largely used for bacteria30 and numerous technical challenges have limited the recovery of eukaryotic genomes with this approach28313233. The most complete assembly obtained so far is for an uncultured stramenopile belonging to the MAST-4 clade and contains about one third of the core eukaryotic gene set33.…”

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confidence: 99%

“…However, this approach has been largely used for bacteria30 and numerous technical challenges have limited the recovery of eukaryotic genomes with this approach28313233. The most complete assembly obtained so far is for an uncultured stramenopile belonging to the MAST-4 clade and contains about one third of the core eukaryotic gene set33. Recently, the Tara Oceans expedition collected water samples from the photic zone of hundreds of marine sites from all oceans and obtained physicochemical parameters, such as silicate, nitrate, phosphate, temperature and chlorophyll343536.…”

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confidence: 99%

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Survey of the green picoalga Bathycoccus genomes in the global ocean

Vannier

Leconte

Seeleuthner

et al. 2016

Sci Rep

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Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.

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confidence: 99%

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confidence: 99%

Survey of the green picoalga Bathycoccus genomes in the global ocean

Vannier

Leconte

Seeleuthner

et al. 2016

Sci Rep

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“…SNVs in kidney tumor MDA Xu et al, 2012 Tumor evolution in breast cancer DOP-PCR Navin et al, 2011 Tumor evolution in breast cancer MDA Wang et al, 2014b Tumor evolution in myeloproliferative neoplasm MDA Hou et al, 2012 CTCs in lung cancer MALBAC Ni et al, 2013 Recombination and aneuploidy in human sperm MALBAC Lu et al, 2012 Recombination and mutation in human sperm MDA Wang et al, 2012 The triads of the first and second polar bodies and oocyte pronuclei MALBAC Hou et al, 2013 Mosaic CNVs in human neurons MDA McConnell et al, 2013 Uncultivable microbes MDA Marcy et al, 2007b;Marshall et al, 2012 Uncultivable protists MDA Yoon et al, 2011;Roy et al, 2014 Single-cell transcriptomic sequencing…”

Section: Single-cell Genomic Sequencingmentioning

confidence: 98%

Single-Cell Sequencing Technologies: Current and Future

Liang

Cai

Sun

2014

Journal of Genetics and Genomics

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“…This is especially challenging when dealing with eukaryotic organisms because their genomes are larger than bacterial genomes and can have long repetitive stretches. Recent studies have found that genome recovery per SAG for MAST-4 flagellate cells ranged between 20 and 40% (Roy et al 2014, Mangot et al 2017. This means that during traditional MDA-based SAG sequencing, not only is a fraction of the host genome missed, but also the genomes of its symbionts can be underrepresented or totally missed.…”

Section: Single-cell Genomicsmentioning

confidence: 99%

Exploring the oceanic microeukaryotic interactome with metaomics approaches

Krabberød¹,

Bjorbækmo²,

Shalchian-Tabrizi³

et al. 2017

Aquat. Microb. Ecol.

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THE MICROBIAL OCEANOur collective awareness of the significance of marine ecosystems has increased steadily during the last 40 yr, progressing in concert with the development of new technologies that have allowed us to dig deeper into the microbial world. A number of key events can be identified from this period, for example the formulation of the microbial-loop concept, the discovery of abundant photoautotrophic (Synechococcus and Prochlorococcus) and heterotrophic (SAR11) pico-sized prokaryotic plankton as well as novel lineages of heterotrophic picoeukaryotes (e.g. MALV and MAST), the recognition of the importance of Archaea in oceanic plankton, the realization that the majority of marine microbes cannot be cultured, the discovery of the rare biosphere and the key role of viruses in oceanic communities (Kirchman 2008 ABSTRACT: Biological communities are systems composed of many interacting parts (species, populations or single cells) that in combination constitute the functional basis of the biosphere. Animal and plant ecologists have advanced substantially our understanding of ecological interactions. In contrast, our knowledge of ecological interaction in microbes is still rudimentary. This represents a major knowledge gap, as microbes are key players in almost all ecosystems, particularly in the oceans. Several studies still pool together widely different marine microbes into broad functional categories (e.g. grazers) and therefore overlook fine-grained species/population-specific interactions. Increasing our understanding of ecological interactions is particularly needed for oceanic microeukaryotes, which include a large diversity of poorly understood symbiotic relationships that range from mutualistic to parasitic. The reason for the current state of affairs is that determining ecological interactions between microbes has proven to be highly challenging. However, recent technological developments in genomics and transcriptomics (metaomics for short), coupled with microfluidics and high-performance computing are making it increasingly feasible to determine ecological interactions at the microscale. Here, we present our views on how this field will advance thanks to the progress in metaomics approaches as well as potential avenues for future research.

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Single cell genome analysis of an uncultured heterotrophic stramenopile

Cited by 43 publications

References 53 publications

Survey of the green picoalga Bathycoccus genomes in the global ocean

Survey of the green picoalga Bathycoccus genomes in the global ocean

Single-Cell Sequencing Technologies: Current and Future

Exploring the oceanic microeukaryotic interactome with metaomics approaches

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