About

The Forest Genomics Laboratory, led by Matias Kirst, focuses on the genomics of plants, including quantitative and population genomics. The lab utilizes genomic and transcriptomic data to support breeding and evolutionary studies, discovering genes that regulate complex traits. They employ biotechnology tools such as CRISPR and next-generation DNA sequencing to accelerate breeding and study gene function. The lab also applies genomic selection methods to simplify the improvement of tree species.

Research topics

• Biology
• Genetics
• Botany
• Cell biology
• Artificial Intelligence
• Computer Science
• Information Retrieval
• Data Mining
• Computational biology
• Evolutionary biology

Selected publications

• Single-nucleus transcriptomics revealed auxin-driven mechanisms of wood plasticity to enhance severe drought tolerance in poplar

  Genome biology · 2025-09-26 · 3 citations

  articleOpen access

  BACKGROUND: Drought significantly affects forests and woody crops by limiting their growth, increasing their susceptibility to diseases, and reducing productivity. Wood anatomical plasticity is a crucial adaptive mechanism that enables trees to cope with fluctuations in water availability. During severe drought, trees develop more and narrower vessels, enhancing hydraulic safety and reducing the risk of embolism. However, the molecular regulation of vessel formation is still not well understood. RESULTS: Using single-nucleus transcriptomics, we have generated a cell type-specific gene expression map of the mature poplar stem under well-watered and drought conditions. Our findings reveal extensive gene expression reprogramming in xylem-forming cells, with changes in auxin homeostasis identified as a key mechanism for anatomical adaptation. Specifically, we show that poplar WAT1-like genes control vessel spatial patterning. Additionally, the downregulation of WAT1-like gene expression in the dividing cells of the vascular cambium and the upregulation of MP-like gene expression in cells undergoing early vessel differentiation facilitate the formation of secondary xylem with narrower and more numerous vessels under drought. Furthermore, the wat2 mutant exhibits greater drought tolerance than wild-type trees, underscoring its potential for developing drought-resilient tree varieties. CONCLUSIONS: This study provides the first single-nucleus transcriptomic map of hybrid poplar stems under severe drought, uncovering auxin-driven hormonal networks that regulate xylem plasticity and enhance drought tolerance. These insights provide valuable targets for improving resilience in poplar and other woody species.

  PublisherOA PDFDOI

• InteracTor: Feature engineering and explainable AI for profiling protein structure-interaction-function relationships

  PLoS Computational Biology · 2025-10-13 · 3 citations

  articleOpen accessCorresponding

  Characterizing protein families' structural and functional diversity is essential for understanding their biological roles. Traditional analyses often focus on primary and secondary structures, which may not fully capture complex protein interactions. Here we introduce InteracTor, a novel toolkit that extracts multimodal features from protein three-dimensional (3D) structures, including interatomic interactions like hydrogen bonds, van der Waals forces, and hydrophobic contacts. By integrating eXplainable Artificial Intelligence (XAI) techniques, we quantified the importance of the extracted features in the classification of protein structural and functional families. InteracTor's interpref features enable mechanistic insights into the determinants of protein structure, function, and dynamics, offering a transparent means to assess their predictive power within machine learning models. Interatomic interaction features extracted by InteracTor demonstrated superior predictive power for protein family classification compared to features based solely on primary or secondary structure, revealing the importance of considering specific tertiary contacts in computational protein analysis. This work provides a robust framework for future studies aiming to enhance the capabilities of models for protein function prediction and drug discovery.

  PublisherDOI

• Deep tissue profiling of Populus stem at single nucleus level reveals uncharacterized cell types and cell-specific gene regulatory networks

  Genome biology · 2025-08-28 · 4 citations

  articleOpen accessSenior authorCorresponding

  BACKGROUND: Single-cell genomics is revolutionizing plant developmental biology, enabling the transcriptome profiling of individual cells and their lineage relationships. However, plant cell walls polymers hamper the dissociation and analysis of intact cells. This rigid structure can conceal cell types embedded in complex, lignified, multi-cell layered tissues such as those undergoing secondary growth. Their absence leads to incomplete single-cell genomic atlases and lineage inferences. RESULTS: We isolate nuclei to capture transcripts representing the diversity of cells throughout the stem of the woody perennial Populus trichocarpa generating a high-resolution transcriptome atlas of cell types and lineage trajectories. RNA sequencing of 11,673 nuclei identifies 26 clusters representing cell types in the cambium, xylem, phloem, and periderm. Comparative analysis with protoplast-derived transcriptome data reveals significant biases, with nuclei-based sequencing providing a higher representation of cells in lignified inner xylem tissues. Among previously underrepresented types, we uncover vessel-associated cells (VAC), a largely uncharacterized parenchyma subtype and the terminus of a xylem cell lineage. Gene regulatory analysis identifies a VAC-specific network and the Populus MYB48 as its primary regulator. Functional validation of MYB48 knockout mutants show an increase in vessel number and size, pointing to a role of VACs in vessel development. CONCLUSIONS: Our study demonstrates the capture and transcriptome characterization of cell types embedded in plant secondary growth, identifying novel regulators of xylem development and stress adaptation. The discovery of MYB48 as a key regulator of VAC function highlights a previously uncharacterized mechanism influencing vessel development, with applications to improving wood formation and stress resilience.

  PublisherOA PDFDOI

• InteracTor: Feature Engineering and Explainable AI for Profiling Protein Structure-Interaction-Function Relationships

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-16 · 1 citations

  preprintOpen access

  ABSTRACT Characterizing protein families’ structural and functional diversity is essential for understanding their biological roles. Traditional analyses often focus on primary and secondary structures, which may not fully capture complex protein interactions. Here we introduce InteracTor, a novel toolkit that extracts multimodal features from protein three-dimensional (3D) structures, including interatomic interactions like hydrogen bonds, van der Waals forces, and hydrophobic contacts. By integrating Explainable AI (XAI) techniques, we quantified the importance of the extracted features in the classification of protein structural and functional families. InteracTor’s interpretable features enable mechanistic insights into the determinants of protein structure, function, and dynamics, offering a transparent means to assess their predictive power within machine learning models. Interatomic interaction features extracted by InteracTor demonstrated superior predictive power for protein family classification compared to features based solely on primary or secondary structure, revealing the importance of considering specific tertiary contacts in computational protein analysis. This work provides a robust framework for future studies aiming to enhance the capabilities of models for protein function prediction and drug discovery. AUTHOR SUMMARY InteracTor is a computational toolkit designed to enhance our understanding of protein structure and function by focusing on three-dimensional (3D) structural interactions. Unlike traditional approaches that primarily rely on sequence or secondary structure data, InteracTor extracts biologically meaningful features such as hydrogen bonds, van der Waals forces, and hydrophobic contacts, which are critical for protein stability and dynamics. By integrating these features into machine learning models alongside explainable AI methods, InteracTor provides interpretable insights into how specific structural interactions influence protein behavior. Our results demonstrate that tertiary structure features significantly improve the accuracy of protein family classification compared to sequence-based methods alone, underscoring the importance of considering 3D interactions in computational protein analyses. The toolkit’s modular design makes it adaptable for diverse applications, including drug discovery and protein engineering. In a broader context, InteracTor bridges the gap between computational biology and practical applications in medicine and biotechnology by offering a transparent and robust framework for analyzing proteins at a molecular level. This work represents a step forward in leveraging structural data to advance predictive modeling and biological discovery.

  PublisherOA PDFDOI

• Convergent evolution of <i>NFP</i> -facilitated root nodule symbiosis

  Proceedings of the National Academy of Sciences · 2025-09-09 · 2 citations

  articleOpen access

  The origin and phylogenetic distribution of symbiotic associations between nodulating angiosperms and nitrogen-fixing bacteria have long intrigued biologists. Recent comparative evolutionary analyses have yielded alternative hypotheses: a multistep pathway of independent gains and losses of root nodule symbiosis vs. a single gain followed by numerous losses. A detailed reconstruction of the history of genes involved in signaling between nitrogen-fixing bacteria and potential hosts, particularly lipo-chitooligosaccharide (LCO) signaling, is needed to distinguish between these hypotheses. LCO recognition by plants involves the Nod Factor Perception ( NFP ) gene family; in the legume model Medicago truncatula (Fabales), MtNFP is essential for establishing rhizobial symbiosis. Here, we document convergent evolution of NFP , indicating multiple origins of LCO-driven symbiosis. In contrast to previous models that explain the recruitment of NFP via a single duplication in the ancestor of the nitrogen-fixing clade, our phylogenomic and synteny results suggest this duplication does not span the entire clade. Tandem duplication in a common ancestor of Cucurbitales and Rosales resulted in the NFP1 and NFP2 groups. In contrast, the phylogenetically closest paralog of MtNFP is MtLYR1 , located on a different chromosome within a large syntenic block. All available data indicate that a large-scale duplication resulted in MtNFP and MtLYR1 , likely corresponding to a whole-genome duplication in an ancestor of subfamily Papilionoideae of Fabaceae. We show that MtNFP and the NFP2 -like group are not orthologous, indicating multiple independent gains of NFP -based LCO signaling. This molecular convergence provides a possible mechanism for multiple gains of root nodule symbiosis across the nitrogen-fixing clade.

  PublisherOA PDFDOI

• Single-nuclei transcriptomics revealed auxin-driven mechanisms of wood plasticity and severe drought tolerance in poplar

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-13 · 3 citations

  preprintOpen access

  ABSTRACT Drought significantly affects forests and woody crops by limiting their growth, increasing their susceptibility to diseases, and reducing productivity. Wood anatomical plasticity is a crucial adaptive mechanism that enables trees to cope with fluctuations in water availability. During severe drought, trees develop more and narrower vessels, enhancing hydraulic safety and reducing the risk of embolism. However, the molecular regulation of vessel formation is still not well understood. Using single-nucleus transcriptomics, we generated a cell type-specific gene expression map of the mature poplar stem under well-watered and drought conditions. Our findings revealed extensive gene expression reprogramming in xylem-forming cells, with changes in auxin homeostasis identified as a key mechanism for anatomical adaptation. Specifically, we showed that poplar WAT1 -like genes control vessel spatial patterning. Additionally, the downregulation of WAT1 -like gene expression in the dividing cells of the vascular cambium and the upregulation of MP -like gene in cells undergoing early vessel differentiation facilitate the formation of secondary xylem with narrower and more numerous vessels. Furthermore, the wat2 mutant exhibited greater drought tolerance than wild-type trees, underscoring its potential for developing drought-resilient tree varieties. These insights enhance our understanding of xylem plasticity and provide valuable targets for improving drought tolerance in woody plants.

  PublisherOA PDFDOI

• A Circadian Light Regulator Controls a Core CAM Gene in the Ice Plant's C3-to-CAM Transition

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-06

  preprintOpen accessSenior authorCorresponding

  Crassulacean acid metabolism (CAM) enhances drought tolerance by shifting carbon fixation to the night, improving water-use efficiency compared to C3 and C4 photosynthesis. However, the molecular regulators of CAM induction remain poorly understood. Here, we generate the first single-nucleus transcriptome atlas of a CAM species, Mesembryanthemum crystallinum, to resolve transcriptional dynamics at the cell-type level during the C3-to-CAM transition. Using snRNA-seq and a 24-hour time-course bulk RNA-seq dataset, we identify PPCK1, a key CAM enzyme regulator, as part of a co-expression network enriched in circadian clock genes and salt-induced pathways. We demonstrate that the ice plant HY5 (McHY5) directly activates PPCK1, a function absent in the C3 model species Arabidopsis thaliana. This discovery reveals a fundamental divergence in transcription factor activity between a CAM and a C3 species, suggesting that CAM evolution in M. crystallinum involved a rewiring of core regulatory elements underlying CAM. Identifying a transcription factor that directly controls a major CAM gene provides a key step toward decoding CAM regulatory architecture and opens new avenues for engineering drought-resilient crops.

  PublisherOA PDFDOI

• Author Correction: Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

  Nature Communications · 2024-08-01 · 1 citations

  erratumOpen access

  Correction to: Nature Communications https://doi.org/10.1038/s41467-024-48036-3, published online 27 May 2024&#13;\nhttp://hdl.handle.net/10261/361232

  PublisherOA PDFDOI

• The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

  Cell Reports · 2024-02-01 · 37 citations

  articleOpen accessSenior authorCorresponding

  Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.

  PublisherOA PDFDOI

• Investigating biological nitrogen fixation via single-cell transcriptomics

  Journal of Experimental Botany · 2024-11-20 · 5 citations

  reviewOpen accessSenior authorCorresponding

  The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is essential for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: (i) single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species; (ii) characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations; (iii) single-cell transcriptomics data have enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization; and (iv) trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis.

  PublisherDOI

Recent grants

• Genome and Transcriptome Based Prediction and Regulator Inference of Molecular and Whole-Plant Phenotypes

  NSF · $2.0M · 2015–2020

• Gene Expression Networks and their Regulators in a Model Perennial Plant

  NSF · $250k · 2008–2010

Frequent coauthors

• Daniel Conde

  Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

  51 shared

• Christopher Dervinis

  University of Florida

  44 shared

• Jöerg Bohlmann

  Canada's Michael Smith Genome Sciences Centre

  43 shared

• John M. Davis

  AAA College of Engineering and Technology

  41 shared

• Márcio F. R. Resende

  37 shared

• Dário Grattapaglia

  Universidade Católica de Brasília

  33 shared

• Leandro G. Neves

  32 shared

• Steven Ralph

  University of North Dakota

  31 shared

Labs

• Matias Kirst LabPI