Research

The secondary xylem, or wood, is the most common natural product on Earth and is formed by the activity of the vascular cambium, a secondary meristem. The development of secondary xylem cells depends on the precise spatial distribution of molecular signals, which vary with the position and type of each developing cell. Forward genetic techniques and functional genomics have identified genes involved in secondary xylem formation. However, the molecular signals and regulatory networks that determine the specific cell fates of tracheary elements, fibers, and parenchyma cells remain poorly understood. Additionally, the molecular mechanisms regulating the flexibility of secondary xylem in response to environmental stresses remain largely unknown.

 

  1. Identification of the molecular basis of the poplar vascular development modifications to cope with drought

Wood anatomy is highly adaptable and responds to drought, often at the expense of growth and quality. We investigate the molecular mechanisms behind this plasticity in poplar using single-cell genomics to analyze how each xylem cell type reacts to water stress. Our goal is to develop more resilient and productive trees for a changing climate.

 

 

Figure 1. (A) Characterization of secondary xylem plasticity in Populus under severe drought, including anatomical changes that enhance drought resistance. (B) Use of single-nucleus transcriptomics to identify regulatory genes controlling drought-induced wood developmental changes. (C) Discovery of new pathways underlying secondary xylem plasticity and development of drought-tolerant trees.

 

In our latest study (https://doi.org/10.1186/s13059-025-03794-1), we generated a comprehensive single-nucleus RNA-seq dataset from mature poplar stems under well-watered and severe drought conditions. To facilitate the exploration and visualization of these data, we have developed an online tool that enables researchers to examine gene expression at single-cell resolution, compare conditions, and explore cell-type-specific transcriptional responses. The tool is freely accessible via the following links:

 

Whole dataset in poplar stem:

https://danielcondelab.shinyapps.io/snrnaseq_drought_tolerance_in_poplar_whole_dataset/.

 

Subset of cells involved in secondary xylem:

https://danielcondelab.shinyapps.io/snrna_seq_drought_tolerance_in_poplar_xylem_subset/. 

 

  1. Unraveling the molecular regulation of vessel size and spatial patterning

The spatial pattern and size of xylem vessels are developmental decisions that define how trees transport water and grow. These patterns do not arise by chance; they result from precise molecular regulation during wood formation. Yet, the core mechanisms that specify which cells become vessels, how wide they grow, and how they are arranged within the secondary xylem remain largely unknown. Our research aims to decode these developmental programs. By integrating high-resolution wood anatomy with single-cell and spatial genomics in Populus, we identify the genes, signals, and regulatory networks that shape vessel patterning. Understanding this developmental control is essential for advancing our ability to design trees with resilient hydraulic architecture in a changing climate.

 

Figure 2. Representative Populus genotypes engineered to alter vessel size and spatial patterning, alongside transverse sections of secondary xylem highlighting changes in vessel organization. These genotypes provide a framework to dissect the developmental programs and regulatory pathways that control vessel differentiation and patterning in wood.

 

 

  1. Applying spatio-temporal gene network studies to infer the mechanisms of chilling measurement in poplar winter bud

 

In temperate trees, once the dormancy period has been established, buds stay dormant until a specific cold period, called the chilling requirement, is met. Climate change threatens to reduce winter chilling, potentially disrupting this process and delaying timely vegetative growth and flowering in key tree species, thereby affecting biomass and fruit production. Our research combines spatio-temporal gene network analyses with transcriptomics and proteomics to uncover the genetic and molecular mechanisms behind dormancy and bud break, offering insights for developing climate-resilient trees.

 

Figure 3. Workflow to study chilling requirement in poplar winter buds. Dormancy is induced under controlled conditions, and buds are collected at different stages of cold exposure. Single-nucleus RNA-seq will reveal cell type-specific transcriptional changes, which will be integrated to identify key regulatory genes and networks controlling dormancy release and bud break. 

 

  1. Soil phytoremediation of heavy metal pollutants by genetically enhanced trees in combination with mutualistic microorganisms

This research aims to implement a phytoremediation strategy for soils contaminated with heavy metals. To develop this strategy, the chosen plant species is poplar (Populus tremula X alba). The project is divided into three specific objectives: 

  1. Generation and selection of genetically improved poplar lines for their accumulation capacity and tolerance to heavy metals.
  2. Selection of mutualistic microorganisms isolated from areas contaminated with heavy metals.
  3. Toxicity tests and accumulation of heavy metals assays in genetically improved poplar lines in combination with selected mutualistic microorganisms.

 

 Figure 4. Heavy metal toxicity assays in poplar wild-type and transgenic lines.



 

Conde Rodríguez, Daniel - Young Investigator Researcher (YIR)

Murillo Murillo, Juan - PhD Student

Redondo López, Arturo - PhD Student

Rodrigo García, Miguel - PhD Student

  • PID2024-161778OB-I00. Tree Growth Optimization by Identifying Molecular Enhancers of Developmental Plasticity for Climate Resilience and Resource Sustainability (Tree-MENDOUS). 2026-2029. Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación (MICIU/AEI), Spain and European Union. PIs: Mariano Perales and Daniel Conde Rodríguez.

      

  • 2023-T1/BIO-29308. Biotechnology applied to adapt woody crops to climate change (AdaptTrees). 2024-2028. César Nombela program of the “Comunidad Autónoma de Madrid” for talent attraction. PI: Daniel Conde Rodríguez.



  • Identifying the molecular regulatory mechanisms of stem cell differentiation during the formation of new organs in trees, by applying single-cell transcriptomics. 2023-2026. La Caixa Junior Leader Fellowship Incoming. PI: Daniel Conde Rodríguez.



Gómez-Soto, D., Pereira, W.J., Piedrabuena-Díaz, A., Dervinis, C., Kirst, M., Allona, I., Perales, M., Conde, D. 2025. Single-nucleus transcriptomics revealed auxin-driven mechanisms of wood plasticity to enhance severe drought tolerance in poplar. Genome Biology 26, 312. DOI: 10.1186/s13059-025-03794-1

Schmidt, H.W., Conde, D., Pereira, W.J., Triozzi, P.M., Balmant, K.M., Dervinis, C., Kirst, M. 2025. Deep tissue profiling of Populus stem at single nucleus level reveals uncharacterized cell types and cell-specific gene regulatory networks. Genome Biology 26, 258. DOI: 10.1186/s13059-025-03728-x

Pereira, W.J., Conde, D., Perron, N., Schmidt, H.W., Dervinis, C., Venado, R.E., Ané, J.-M., Kirst, M. 2024. Investigating biological nitrogen fixation via single-cell transcriptomics. Journal of Experimental Botany erae454. DOI: 10.1093/jxb/erae454

Kates, H.R., O’Meara, B.C., LaFrance, R., Stull, G.W., James, E.K., Liu, S.-Y., Tian, Q., Yi, T.-S., Conde, D., Kirst, M., Ané, J.-M., Soltis, D.E., Guralnick, R.P., Soltis, P.S., Folk, R.A. 2024. Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants. Nature Communications 15, 4262. DOI: 10.1038/s41467-024-48036-3

Pereira, W.J., Boyd, J., Conde, D., Triozzi, P.M., Balmant, K.M., Dervinis, C., Schmidt, H.W., Boaventura-Novaes, C., Chakraborty, S., Knaack, S.A., Gao, Y., Feltus, F.A., Roy, S., Ané, J.-M., Frugoli, J., Kirst, M. 2024. The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula. Cell Reports 43, 113747. DOI: 10.1016/j.celrep.2024.113747

Pereira, W.J., Conde, D., Perron, N., Schmidt, H.W., Dervinis, C., Venado, R.E., Ané, J.-M., Kirst, M. 2024. Investigating biological nitrogen fixation via single-cell transcriptomics. Journal of Experimental Botany erae454. DOI: 10.1093/jxb/erae454

Sreedasyam, A., Plott, C., Hossain, M.S., Lovell, J.T., Grimwood, J., Jenkins, J.W., Daum, C., Barry, K., Carlson, J., Shu, S., Phillips, J., Amirebrahimi, M., Zane, M., Wang, M., Goodstein, D., Haas, F.B., Hiss, M., Perroud, P.-F., Jawdy, S.S., Yang, Y., Hu, R., Johnson, J., Kropat, J., Gallaher, S.D., Lipzen, A., Shakirov, E.V., Weng, X., Torres-Jerez, I., Weers, B., Conde, D., Pappas, M.R., Liu, L., Muchlinski, A., Jiang, H., Shyu, C., Huang, P., Sebastian, J., Laiben, C., Medlin, A., Carey, S., Carrell, A.A., Chen, J.-G., Perales, M., Swaminathan, K., Allona, I., Grattapaglia, D., Cooper, E.A., Tholl, D., Vogel, J.P., Weston, D.J., Yang, X., Brutnell, T.P., Kellogg, E.A., Baxter, I., Udvardi, M., Tang, Y., Mockler, T.C., Juenger, T.E., Mullet, J., Rensing, S.A., Tuskan, G.A., Merchant, S.S., Stacey, G., Schmutz, J. 2023. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Nucleic Acids Research 51, 8383–8401. DOI: 10.1093/nar/gkad616

Vigneaud, J., Kohler, A., Sow, M.D., Delaunay, A., Fauchery, L., Guinet, F., Daviaud, C., Barry, K.W., Keymanesh, K., Johnson, J., Singan, V., Grigoriev, I., Fichot, R., Conde, D., Perales, M., Tost, J., Martin, F.M., Allona, I., Strauss, S.H., Veneault-Fourrey, C., Maury, S. 2023. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus. New Phytologist. DOI: 10.1111/nph.18734

Conde, D., Kirst, M. 2022. Decoding exceptional plant traits by comparative single-cell genomics. Trends in Plant Science 27, 1095–1098. DOI: 10.1016/j.tplants.2022.08.006

Conde, D., Triozzi, P.M., Pereira, W.J., Schmidt, H.W., Balmant, K.M., Knaack, S.A., Redondo-López, A., Roy, S., Dervinis, C., Kirst, M. 2022. Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus. Development 149, dev200632. DOI: 10.1242/dev.200632

Vigneaud, J., Kohler, A., Sow, M.D., Delaunay, A., Fauchery, L., Guinet, F., Daviaud, C., Barry, K.W., Keymanesh, K., Johnson, J., Singan, V., Grigoriev, I., Fichot, R., Conde, D., Perales, M., Tost, J., Martin, F.M., Allona, I., Strauss, S.H., Veneault-Fourrey, C., Maury, S. n.d. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus. New Phytologist n/a. DOI: 10.1111/nph.18734

Knaack, S.A., Conde, D., Chakraborty, S., Balmant, K.M., Irving, T.B., Maia, L.G.S., Triozzi, P.M., Dervinis, C., Pereira, W.J., Maeda, J., Schmidt, H.W., Ané, J.-M., Kirst, M., Roy, S. 2022. Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula. BMC Biology 20, 252. DOI: 10.1186/s12915-022-01450-9

Irving, T.B., Chakraborty, S., Maia, L.G.S., Knaack, S., Conde, D., Schmidt, H.W., Triozzi, P.M., Simmons, C.H., Roy, S., Kirst, M., Ané, J.-M. 2022. An LCO-responsive homolog of NODULE INCEPTION positively regulates lateral root formation in Populus sp.. Plant Physiology 190, 1699–1714. DOI: 10.1093/plphys/kiac356

Pereira, W.J., Knaack, S., Chakraborty, S., Conde, D., Folk, R.A., Triozzi, P.M., Balmant, K.M., Dervinis, C., Schmidt, H.W., Ané, J.-M., Roy, S., Kirst, M. 2022. Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade. New Phytologist 234, 634–649. DOI: 10.1111/nph.18006

Triozzi, P.M., Irving, T.B., Schmidt, H.W., Keyser, Z.P., Chakraborty, S., Balmant, K., Pereira, W.J., Dervinis, C., Mysore, K.S., Wen, J., Ané, J.-M., Kirst, M., Conde, D. 2022. Spatiotemporal cytokinin response imaging and ISOPENTENYLTRANSFERASE 3 function in Medicago nodule development. Plant Physiology 188, 560–575. DOI: 10.1093/plphys/kiab447

Pereira, W.J., Almeida, F.M., Conde, D., Balmant, K.M., Triozzi, P.M., Schmidt, H.W., Dervinis, C., Pappas, G.J., Kirst, M. 2021. Asc-Seurat: analytical single-cell Seurat-based web application. BMC Bioinformatics 22, 556. DOI: 10.1186/s12859-021-04472-2

Triozzi, P.M., Schmidt, H.W., Dervinis, C., Kirst, M., Conde, D. 2021. Simple, efficient and open-source CRISPR/Cas9 strategy for multi-site genome editing in Populus tremula × alba. Tree Physiology 41, 2216–2227. DOI: 10.1093/treephys/tpab066

Conde, D., Triozzi, P.M., Balmant, K.M., Doty, A.L., Miranda, M., Boullosa, A., Schmidt, H.W., Pereira, W.J., Dervinis, C., Kirst, M. 2021. A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus. PLOS ONE 16, e0251149. DOI: 10.1371/journal.pone.0251149

Gómez-Soto, D., Ramos-Sánchez, J.M., Alique, D., Conde, D., Triozzi, P.M., Perales, M., Allona, I. 2021. Overexpression of a SOC1-Related Gene Promotes Bud Break in Ecodormant Poplars. Frontiers in Plant Science 12.

Balmant, K.M., Noble, J.D., Alves, F.C., Dervinis, C., Conde, D., Schmidt, H.W., Vazquez, A.I., Barbazuk, W.B., Campos, G. de los, Resende, M.F.R., Kirst, M. 2020. Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides. Genome Research 30, 1131–1143. DOI: 10.1101/gr.261438.120

Ribeiro, C.L., Conde, D., Balmant, K.M., Dervinis, C., Johnson, M.G., McGrath, A.P., Szewczyk, P., Unda, F., Finegan, C.A., Schmidt, H.W., Miles, B., Drost, D.R., Novaes, E., Gonzalez-Benecke, C.A., Peter, G.F., Burleigh, J.G., Martin, T.A., Mansfield, S.D., Chang, G., Wickett, N.J., Kirst, M. 2020. The uncharacterized gene EVE contributes to vessel element dimensions in Populus. Proceedings of the National Academy of Sciences 117, 5059–5066. DOI: 10.1073/pnas.1912434117

Conde, D., Perales, M., Sreedasyam, A., Tuskan, G.A., Lloret, A., Badenes, M.L., González-Melendi, P., Ríos, G., Allona, I. 2019. Engineering Tree Seasonal Cycles of Growth Through Chromatin Modification. Frontiers in Plant Science 10.