Comparative regulomics of wood formation across dicot and conifer trees
Abstract
Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource for wood transcriptomes spanning multiple dicots and conifers, representing the two major tree-containing lineages separated by more than 300 million years of evolution. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred candidate regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.
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BibTeX
@article{rodriguez2026comparative,
title = {{Comparative regulomics of wood formation across dicot and conifer trees}},
author = {Eduardo Rodriguez and Siri Birkeland and Ellen Dimmen Chapple and Samuel Fredriksson and Zulema Carracedo Lorenzo and Teitur Ahlgren Kalman and Vikash Kumar and Jamie Mccann and Jason Hill and Sivagamy Soundiramourtty and Aline Voxeur and Åsmund Kjendseth Røhr and Hannele Tuominen and Ewa Mellerowicz and Nathaniel Street and Torgeir Hvidsten},
journal = {Nature Communications},
year = {2026},
month = jul,
doi = {10.1038/s41467-026-75624-2},
url = {https://hal.science/hal-05785417v1},
note = {CC BY},
}
RIS
TY - JOUR
TI - Comparative regulomics of wood formation across dicot and conifer trees
AU - Eduardo Rodriguez
AU - Siri Birkeland
AU - Ellen Dimmen Chapple
AU - Samuel Fredriksson
AU - Zulema Carracedo Lorenzo
AU - Teitur Ahlgren Kalman
AU - Vikash Kumar
AU - Jamie Mccann
AU - Jason Hill
AU - Sivagamy Soundiramourtty
AU - Aline Voxeur
AU - Åsmund Kjendseth Røhr
AU - Hannele Tuominen
AU - Ewa Mellerowicz
AU - Nathaniel Street
AU - Torgeir Hvidsten
PY - 2026
DA - 2026/07/22
JO - Nature Communications
DO - 10.1038/s41467-026-75624-2
UR - https://hal.science/hal-05785417v1
AB - Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource for wood transcriptomes spanning multiple dicots and conifers, representing the two major tree-containing lineages separated by more than 300 million years of evolution. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred candidate regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.
SN - 2041-1723
SN - 2041-1723
ER -