The structural history of Eukarya
- 1The Department of Molecular Biosciences, The Wenner-Gren Institute. Stockholm University, Svante Arrhenius väg 20C, 114 18 Stockholm.
- 2Science for Life Laboratory, Solna 171 65, Sweden.
Abstract
Comparative genomics has traditionally relied on sequence-based markers, yet the global evolutionary landscape of protein architecture remains largely unexplored. We present the Structural History of Eukarya (SHE), a structural similarity-derived phylogeny from all-vs-all structural comparisons on the proteome level of 1542 eukaryotic species, encompassing nearly 300 trillion pairwise protein alignments. This proteome-scale analysis reveals a bipartite model of eukaryotic evolution: a rigid Strict Core dominated by cytoskeletal architecture, supporting a more plastic Operational Engine centered on translational machinery. We identify lineage-specific accelerations of structural evolution in species such as birds and ants that are decoupled from proteome expansion. Finally, we demonstrate that proteome-wide structural fidelity enables the functional annotation of uncharacterized proteins and a data-driven framework for model organism selection, replacing heuristic choices with quantitative matching to human biological processes. SHE is freely accessible as an interactive portal.
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BibTeX
@article{daumiller2026structural,
title = {{The structural history of Eukarya}},
author = {Diandra Daumiller and Qiuzhen Li and Patrick Bryant},
journal = {Science Advances},
year = {2026},
month = oct,
doi = {10.1126/sciadv.aeh2524},
url = {https://www.science.org/doi/abs/10.1126/sciadv.aeh2524},
note = {CC BY},
}
RIS
TY - JOUR
TI - The structural history of Eukarya
AU - Diandra Daumiller
AU - Qiuzhen Li
AU - Patrick Bryant
PY - 2026
DA - 2026/10/28
JO - Science Advances
DO - 10.1126/sciadv.aeh2524
UR - https://www.science.org/doi/abs/10.1126/sciadv.aeh2524
AB - Comparative genomics has traditionally relied on sequence-based markers, yet the global evolutionary landscape of protein architecture remains largely unexplored. We present the Structural History of Eukarya (SHE), a structural similarity-derived phylogeny from all-vs-all structural comparisons on the proteome level of 1542 eukaryotic species, encompassing nearly 300 trillion pairwise protein alignments. This proteome-scale analysis reveals a bipartite model of eukaryotic evolution: a rigid Strict Core dominated by cytoskeletal architecture, supporting a more plastic Operational Engine centered on translational machinery. We identify lineage-specific accelerations of structural evolution in species such as birds and ants that are decoupled from proteome expansion. Finally, we demonstrate that proteome-wide structural fidelity enables the functional annotation of uncharacterized proteins and a data-driven framework for model organism selection, replacing heuristic choices with quantitative matching to human biological processes. SHE is freely accessible as an interactive portal.
SN - 2375-2548
ER -