Skip to Main content Skip to Navigation
Journal articles

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.
Document type :
Journal articles
Complete list of metadatas

Cited literature [71 references]  Display  Hide  Download

https://hal.sorbonne-universite.fr/hal-01466618
Contributor : Gestionnaire Hal-Upmc <>
Submitted on : Monday, February 13, 2017 - 4:15:31 PM
Last modification on : Saturday, December 26, 2020 - 1:46:06 PM

File

srep41498.pdf
Publication funded by an institution

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Citation

Jean-François Mangot, Ramiro Logares, Pablo Sánchez, Fran Latorre, Yoann Seeleuthner, et al.. Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells. Scientific Reports, Nature Publishing Group, 2017, 7, pp.41498. ⟨10.1038/srep41498⟩. ⟨hal-01466618⟩

Share

Metrics

Record views

2445

Files downloads

871