Comparative regulomics provides novel insight into the evolution of wood formation across dicot and conifer trees

Rodriguez, E.; Birkeland, S.; Chapple, E. D.; Fredriksson, S.; Lorenzo, Z. C.; Kalman, T. A.; Kumar, V.; Hill, J.; Tuominen, H.; Mellerowicz, E. J.; Street, N. R.; Hvidsten, T. R.

doi:10.1101/2025.06.28.661522

bioRxiv · 10.1101/2025.06.28.661522

Comparative regulomics provides novel insight into the evolution of wood formation across dicot and conifer trees

Rodriguez, E.·Birkeland, S.·Chapple, E. D.·Fredriksson, S.·Lorenzo, Z. C.·Kalman, T. A.·Kumar, V.·Hill, J.·Tuominen, H.·Mellerowicz, E. J.·Street, N. R.·Hvidsten, T. R.

View original source ↗Export metadata ↓

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 spanning the wood transcriptomes of six tree species - three dicots and three conifers - capturing 250 million years of evolutionary divergence. 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 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 foundational resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Rodriguez, E., Birkeland, S., Chapple, E. D., Fredriksson, S., Lorenzo, Z. C., Kalman, T. A., Kumar, V., Hill, J., Tuominen, H., Mellerowicz, E. J., Street, N. R., Hvidsten, T. R.. 2025-06-30. Comparative regulomics provides novel insight into the evolution of wood formation across dicot and conifer trees. https://doi.org/10.1101/2025.06.28.661522

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗

bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗

bioRxiv2026

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains unclear, in part due to the difficulty of achieving gene-specific perturbation of highly conserved loci. Here, we developed an inducible CRISPR interference platform and a custom single-guide RNA (sgRNA) library enabling gene-specific targeting of Pol III-transcribed genes and Pol III machinery. Genome-wide screening identified several Pol III dependencies in diploid fibroblasts and HEK293T cells, including multiple initiator methionine tRNA genes among the strongest fitness dependencies. Unexpectedly, glioblastoma models remained largely insensitive to repression of both individual Pol III genes and core Pol III components, despite efficient target repression. These findings establish a general strategy for gene-specific interrogation of conserved Pol III genes and indicate that glioblastoma models tolerate extensive perturbation of Pol III genes and machinery.

genomics↗