Comparative regulomics of wood formation across dicot and conifer trees

Comparative regulomics of wood formation across dicot and conifer trees. Rodriguez, E., Birkeland, S., Chapple, E. D., Fredriksson, S., Carracedo Lorenzo, Z., Ahlgren Kalman, T., Kumar, V., Mccann, J., Hill, J., Soundiramourtty, S., Voxeur, A., Røhr, Å. K., Tuominen, H., Mellerowicz, E. J., Street, N. R., & Hvidsten, T. R. Nature Communications, Nature Publishing Group, July, 2026.

Paper doi abstract bibtex

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.

@article{rodriguez_comparative_2026,
	title = {Comparative regulomics of wood formation across dicot and conifer trees},
	copyright = {2026 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-026-75624-2},
	doi = {10.1038/s41467-026-75624-2},
	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.},
	language = {en},
	urldate = {2026-07-24},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Rodriguez, Eduardo and Birkeland, Siri and Chapple, Ellen Dimmen and Fredriksson, Samuel and Carracedo Lorenzo, Zulema and Ahlgren Kalman, Teitur and Kumar, Vikash and Mccann, Jamie and Hill, Jason and Soundiramourtty, Sivagamy and Voxeur, Aline and Røhr, Åsmund Kjendseth and Tuominen, Hannele and Mellerowicz, Ewa J. and Street, Nathaniel R. and Hvidsten, Torgeir R.},
	month = jul,
	year = {2026},
	keywords = {Comparative genomics, Gene regulatory networks, Plant evolution, Plant genetics},
}

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