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Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom

View ORCID ProfileMatthieu Muffato, View ORCID ProfileAlexandra Louis, Nga Thi Thuy Nguyen, Joseph Lucas, View ORCID ProfileCamille Berthelot, View ORCID ProfileHugues Roest Crollius
doi: https://doi.org/10.1101/2022.02.17.480882
Matthieu Muffato
1Institut de Biologie de l’École Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, 75005 Paris, France
2Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA, Hinxton, United Kingdom
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Alexandra Louis
1Institut de Biologie de l’École Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, 75005 Paris, France
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Nga Thi Thuy Nguyen
1Institut de Biologie de l’École Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, 75005 Paris, France
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Joseph Lucas
1Institut de Biologie de l’École Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, 75005 Paris, France
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Camille Berthelot
1Institut de Biologie de l’École Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, 75005 Paris, France
3Institut Pasteur, Université de Paris, CNRS UMR3525, INSERM UA12, Comparative Functional Genomics group, F-75015 Paris, France
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  • For correspondence: hrc@bio.ens.psl.eu
Hugues Roest Crollius
1Institut de Biologie de l’École Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, 75005 Paris, France
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  • For correspondence: hrc@bio.ens.psl.eu
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Abstract

Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies, and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organisations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organisations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic and in silico reconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and inter-chromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* First authors

  • https://www.genomicus.bio.ens.psl.eu/genomicus

  • https://github.com/DyogenIBENS/Agora

  • https://sandbox.zenodo.org/record/962110

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted February 19, 2022.
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Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom
Matthieu Muffato, Alexandra Louis, Nga Thi Thuy Nguyen, Joseph Lucas, Camille Berthelot, Hugues Roest Crollius
bioRxiv 2022.02.17.480882; doi: https://doi.org/10.1101/2022.02.17.480882
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Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom
Matthieu Muffato, Alexandra Louis, Nga Thi Thuy Nguyen, Joseph Lucas, Camille Berthelot, Hugues Roest Crollius
bioRxiv 2022.02.17.480882; doi: https://doi.org/10.1101/2022.02.17.480882

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