Reconstruction of ancestral plant genomes for inter-crop translational research
Abstract
We present an initial exploratory framework, Ancestral Genome Reconstruction (AGR), to automatically infer ‘paleogenomes’ from large comparative datasets. By analyzing 84 extant angiosperm species, we reconstructed 10 key ancestral plant genomes of millions of years old. These reconstructed ancestors were instrumental in (i) estimating when emerged the angiosperms as well as major botanical families as well as ancestral shared whole genome duplication events, (ii) tracing the evolutionary trajectories of ancestral chromosomes as well as genes, especially those that may have driven the emergence of key life history traits (exemplifies with woody vs. herbaceous, aquatic vs. terrestrial, C3 vs. C4 and symbiotic root nodulators vs. non-nodulators species). We demonstrate that these paleogenomes serve as tractable backbones for inter-crop translational research, in delivering though an open access web tool (OrthoViewer) genes that have conserved the same ancestral genomic context favoring the identification of ‘phenologs’ -genes underlying similar phenotypes, traits, or processes across species- exemplified with FUWA for yield components, FLC for flowering time, and DDM1 for DNA methylation. Taken together, this study provides a testable paleogenomics workflow, opening novel avenues to integrate evolutionary genomics data into modern climate-smart breeding and support the agroecological transition.
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BibTeX
@article{siguret2026reconstruction,
title = {{Reconstruction of ancestral plant genomes for inter-crop translational research}},
author = {Cléa Siguret and Margaux Olivier and Cécile Huneau and Mamadou Dia Sow and Pierre-Louis Stenger and Christophe Klopp and Marie-Laure Martin and Jean-Philippe Tamby and Sergueï Gorbounov and Raphaël Flores and Fabrice Legeai and Matéo Boudet and Raffaella Battaglia and Davide Guerra and Peter Civan and Caroline Pont and Anne-Françoise Adam-Blondon and Luigi Cattivelli and Olivier Mathieu and Jérôme Salse},
journal = {Molecular Plant},
year = {2026},
month = jul,
doi = {10.1016/j.molp.2026.06.012},
url = {https://hal.science/hal-05682039v2},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Reconstruction of ancestral plant genomes for inter-crop translational research
AU - Cléa Siguret
AU - Margaux Olivier
AU - Cécile Huneau
AU - Mamadou Dia Sow
AU - Pierre-Louis Stenger
AU - Christophe Klopp
AU - Marie-Laure Martin
AU - Jean-Philippe Tamby
AU - Sergueï Gorbounov
AU - Raphaël Flores
AU - Fabrice Legeai
AU - Matéo Boudet
AU - Raffaella Battaglia
AU - Davide Guerra
AU - Peter Civan
AU - Caroline Pont
AU - Anne-Françoise Adam-Blondon
AU - Luigi Cattivelli
AU - Olivier Mathieu
AU - Jérôme Salse
PY - 2026
DA - 2026/07/01
JO - Molecular Plant
DO - 10.1016/j.molp.2026.06.012
UR - https://hal.science/hal-05682039v2
AB - We present an initial exploratory framework, Ancestral Genome Reconstruction (AGR), to automatically infer ‘paleogenomes’ from large comparative datasets. By analyzing 84 extant angiosperm species, we reconstructed 10 key ancestral plant genomes of millions of years old. These reconstructed ancestors were instrumental in (i) estimating when emerged the angiosperms as well as major botanical families as well as ancestral shared whole genome duplication events, (ii) tracing the evolutionary trajectories of ancestral chromosomes as well as genes, especially those that may have driven the emergence of key life history traits (exemplifies with woody vs. herbaceous, aquatic vs. terrestrial, C3 vs. C4 and symbiotic root nodulators vs. non-nodulators species). We demonstrate that these paleogenomes serve as tractable backbones for inter-crop translational research, in delivering though an open access web tool (OrthoViewer) genes that have conserved the same ancestral genomic context favoring the identification of ‘phenologs’ -genes underlying similar phenotypes, traits, or processes across species- exemplified with FUWA for yield components, FLC for flowering time, and DDM1 for DNA methylation. Taken together, this study provides a testable paleogenomics workflow, opening novel avenues to integrate evolutionary genomics data into modern climate-smart breeding and support the agroecological transition.
SN - 1674-2052
SN - 1752-9867
ER -