Ancient animal genome architecture reflects cell type identities


The level of conservation of ancient metazoan gene order (synteny) is remarkable. Despite this, the functionality of the vast majority of such regions in metazoan genomes remains elusive. Utilizing recently published single-cell expression data from several anciently diverging metazoan species, we reveal the level of correspondence between cell types and genomic synteny, identifying genomic regions conferring ancient cell type identity.

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Fig. 1: Microsynteny detection and co-expression signal enrichment.
Fig. 2: The expression of genes in orthologous microsyntenic clusters helps distinguish ancient cell type relationships.

Data availability

Single-cell datasets used in this study are available via gene expression omnibus accessions GSE95723 and GSE111068 and

Code availability

The analysis code is available at


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Computation was done at the Life Science Compute Cluster at the University of Vienna. This work was funded by grants from the Austrian Science Fund to U.T. (P27353) and O.S. (P32190).

Author information

O.S. and B.Z. designed the analyses. B.Z. performed the synteny and expression analyses. B.Z., O.S. and N.S.M.R. analysed the data. B.Z., U.T. and O.S. wrote the manuscript.

Correspondence to Oleg Simakov.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–8.

Reporting Summary

Supplementary Data 1

Synteny blocks.

Supplementary Data 2

Expression data for 32 shared microsyntenic blocks.

Supplementary Data 3

High-resolution vector images for Supplementary Figs. 3–7.

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