About

Wendell Pereira joined the School of Forest, Fisheries, and Geomatics Sciences at the University of Florida in 2024 as a Research Assistant Professor. He develops his research as part of the Forest Genomics Laboratory, where he applies his expertise in biotechnology and bioinformatics to plant science. Dr. Pereira's research integrates cutting-edge genomics, transcriptomics, and proteomics with robust computational methods to investigate complex plant traits relevant to agricultural and ecological improvement. His primary research areas include applied genomic research, which involves investigating the genetic and cellular mechanisms that regulate plant developmental processes and symbiotic interactions with the goal of engineering improved organisms, and tool development, which focuses on creating and implementing novel computational pipelines and accessible software tools to facilitate the analysis, interpretation, and visualization of complex biological data.

Research topics

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

Selected publications

• 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 access

  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

• 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 access

  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

• 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

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

  Cell Reports · 2024-02-01 · 37 citations

  articleOpen access1st author

  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 access1st 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

• Mesophyll-Specific Circadian Dynamics of CAM Induction in the Ice Plant Unveiled by Single-Cell Transcriptomics

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-01-08 · 10 citations

  preprintOpen access

  ABSTRACT Crassulacean acid metabolism (CAM) is an evolutionary modification of the C 3 photosynthetic carbon dioxide fixation pathway used by approximately 7% of terrestrial plants to live in drought-prone environments. Facultative CAM species, such as Mesembryanthemum crystallinum (common ice plant), possess the unique ability to switch from C 3 to CAM photosynthesis in response to high-salinity and water-deficit stress. Here we characterized the environmentally-triggered transition from C 3 to CAM in the ice plant using single nucleus RNA sequencing (snRNA-seq) to identify its putative regulators, supported by a novel high-quality assembled and annotated genome. Analysis of snRNA-seq datasets from ice plant leaves transitioning between C 3 and CAM collected at dawn and dusk revealed substantial transcriptional changes in mesophyll cells at the onset of CAM induction. Notably, our findings identify mesophyll sub-cell types engaged in either CAM or C 3 photosynthesis at dusk. Cell trajectory inference analysis reconstructed both 24-hour CAM and C 3 cycles, enabling a direct comparison of gene expression profiles in these pathways. This comparative study uncovered divergent expression patterns of key circadian clock genes in CAM and C 3 cell trajectories, pointing to a connection between circadian regulation and CAM induction.

  PublisherOA PDFDOI

• Mesophyll-Specific Circadian Dynamics of CAM Induction in the Ice Plant Unveiled by Single-Cell Transcriptomics

  Research Square · 2024-01-08 · 4 citations

  preprintOpen access
  PublisherOA PDFDOI

• Complementary files - The Single-Cell Transcriptome Program of Nodule Development Cellular Lineages in <i>Medicago truncatula</i>

  Figshare · 2024-01-01

  datasetOpen access1st authorCorresponding

  RDS files containing the clustered datasets from "The Single-Cell Transcriptome Program of Nodule Development Cellular Lineages in <i>Medicago truncatula</i>"

  PublisherDOI

• Computational Protocol for DNA Methylation Profiling in Plants Using Restriction Enzyme-Based Genome Reduction

  Methods in molecular biology · 2023-01-01

  article1st author
  PublisherDOI

Frequent coauthors

• Daniel Conde

  Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

  29 shared

• Rosana Pereira Vianello

  27 shared

• Cláudio Brondani

  Brazilian Agricultural Research Corporation

  25 shared

• Paolo M. Triozzi

  Scuola Superiore Sant'Anna

  21 shared

• Christopher Dervinis

  University of Florida

  21 shared

• Matias Kirst

  University of Florida

  21 shared

• Paula Arielle Mendes Ribeiro Valdisser

  Brazilian Agricultural Research Corporation

  19 shared

• Henry W. Schmidt

  University of Florida

  19 shared

Education

• Ph.D. in Molecular Biology

  University of Brasília

  2020

• M. Sc. in Biological Sciences

  Federal University of Goiás

  2016

• B. Sc. in Biotechnology

  Federal University of Goiás

  2014