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. 2019 Nov 25;374(1786):20190082.
doi: 10.1098/rstb.2019.0082. Epub 2019 Oct 7.

A Single-Cell Genome Perspective on Studying Intracellular Associations in Unicellular Eukaryotes

Free PMC article

A Single-Cell Genome Perspective on Studying Intracellular Associations in Unicellular Eukaryotes

Tomáš Tyml et al. Philos Trans R Soc Lond B Biol Sci. .
Free PMC article


Single-cell genomics (SCG) methods provide a unique opportunity to analyse whole genome information at the resolution of an individual cell. While SCG has been extensively used to investigate bacterial and archaeal genomes, the technique has been rarely used to access the genetic makeup of uncultivated microbial eukaryotes. In this regard, the use of SCG can provide a wealth of information; not only do the methods allow exploration of the genome, they can also help elucidate the relationship between the cell and intracellular entities extant in nearly all eukaryotes. SCG enables the study of total eukaryotic cellular DNA, which in turn allows us to better understand the evolutionary history and diversity of life, and the physiological interactions that define complex organisms. This article is part of a discussion meeting issue 'Single cell ecology'.

Keywords: cultivation bias; endosymbiont; giant viruses; intracellular associations; single-cell genomics; unicellular eukaryotes.

Conflict of interest statement

The authors declare no competing interests.


Figure 1.
Figure 1.
(a) Schematic relationships among the major eukaryotic groups (based on Adl et al. [21]). Lineages with intracellular entities identified by the SCG approach are in bold and highlighted in yellow. (b) Numbers of sequenced genomes of three groups of obligately intracellular parasites of eukaryotes (Chlamydiae, Rickettsiales, and giant viruses (defined here as members of double stranded DNA viruses with a genome greater than 0.2 Mb)) are displayed if their host is known (host clades are indicated by colour). Genomic data (genome size, host) were retrieved from JGI genome ( and NCBI genome ( portals on 21 January 2019 or, when missing, from their respective publications.

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  • Single cell ecology.
    Richards TA, Massana R, Pagliara S, Hall N. Richards TA, et al. Philos Trans R Soc Lond B Biol Sci. 2019 Nov 25;374(1786):20190076. doi: 10.1098/rstb.2019.0076. Epub 2019 Oct 7. Philos Trans R Soc Lond B Biol Sci. 2019. PMID: 31587644 Free PMC article.


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