Biology subjects

Triozzi, P. M.

Publications and source records attributed to Triozzi, P. M..

8 recordsLinked to original sources

bioRxiv2025

OVEREXPRESSION OF TEMPRANILLO-LIKE PROTEINS PROMOTES ENDORMANCY RELEASE IN POPLAR

Trees in temperate and boreal latitudes synchronize their growth-dormancy cycles with seasonal environmental variations to ensure their survival over the years. Dormancy control is crucial during winter when plants cease growth and establish buds to protect their apical meristems from cold temperatures. To overcome endormancy, initiate bud break, and restore growth, plants must be exposed to a specific duration of chilling, referred to as the chilling requirement, which is species- and ecotype-dependent. In this work, we study the novel roles of two TEMPRANILLO-like genes (TEML1 and TEML2) in the annual cycle of poplar. We demonstrated that Populus TEML genes are regulated by photoperiod, cold temperatures and the circadian clock, and they play a role in the control of endodormancy. Notably, their function diverges from the role of its Arabidopsis ortholog AtTEM, which regulates FLOWERING LOCUS T (FT) transcription and the photoperiodic flowering transcription. Transcriptomic analysis of endodormant buds during winter revealed that the activation of TEML1 and TEML2 promotes endodormancy release by modulating the expression of endodormancy regulators and growth-promoting genes.

plant biology↗

bioRxiv2024

Genotype-environment association across precipitation regimens reveals the mechanism of plant adaptation to rainy environments

In an era characterized by rapidly changing and less-predictable weather conditions fueled by the climate crisis, understanding the mechanisms underlying local adaptation in plants is of paramount importance for the conservation of species. As the frequency and intensity of extreme precipitation events increase, so are the flooding events resulting from soil water saturation. The deriving onset of hypoxic stress is one of the leading causes of crop damage and yield loss. By combining genomics and remote sensing data, today it is possible to probe natural plant populations that have evolved in different rainfall regimes and look for molecular adaptation to hypoxia. Here, using an environmental genome-wide association study (eGWAS) on 934 non-redundant georeferenced Arabidopsis ecotypes, we have identified functional variants for the gene MED25 BINDING RING-H2 PROTEIN 1 (MBR1). This is a ubiquitin-protein ligase that regulates MEDIATOR25 (MED25), part of a multiprotein complex that interacts with transcription factors which act as key drivers of the hypoxic response in Arabidopsis, namely the RELATED TO AP2 proteins, RAP2.2 and RAP2.12. Through experimental validation, we show that natural variants of MBR1 have a differential impact on the stability of MED25 and, in turn, on hypoxic tolerance. Our study also highlights the pivotal role of the MBR1/MED25 module in establishing a comprehensive hypoxic response. Our findings show that molecular candidates for plant environmental adaptation can be effectively mined from large datasets. This thus supports the need for the integration of forward and reverse genetics with robust molecular physiology validation of the outcomes.

genetics↗

bioRxiv2023

The Single-Cell Transcriptome Program of Nodule Development Cellular Lineages in Medicago truncatula

Legumes can establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules after root exposure to lipo-chito-oligosaccharides secreted by the bacteria. Nodule development initiates with anticlinal mitotic divisions in the pericycle and endodermal and inner cortical cells, establishing cell lineages that ultimately form each nodule compartment. We characterized these lineages by isolating and sequencing the transcriptome of Medicago truncatula single nuclei derived from uninoculated roots and roots undergoing early nodule development at 24, 48, and 96 hours after inoculation. To enrich samples for cells responding to the rhizobia, we complemented the analysis of the Medicago wild-type genotype A17 with a mutant for the autoregulation of nodulation, sunn-4. Analysis of cell lineage trajectories derived from the cortex indicates that their transcriptome is initially enriched for cytokinin perception and signaling while repressing auxin accumulation. As these cells differentiate to form nodules, expression of genes related to auxin biosynthesis, transport, and signaling was enhanced, while genes involved in cytokinin degradation were activated as lineages bifurcated to form the nodule meristem and infection zones. While the contribution of auxin and cytokinin in nodule development has been recognized, this single-cell resource quantifies the expression of each of their regulators, receptors and targets as cells divide and differentiate to form each nodule compartment.

plant biology↗

bioRxiv2021

Single-cell analysis resolves the genetic program of primary vascular system formation in hybrid poplar

Despite the enormous potential of novel approaches to explore gene expression at a single-cell level, we lack a high-resolution and cell type-specific gene expression map of the shoot apex in woody perennials. We use single-nuclei RNA sequencing to determine the cell type-specific transcriptome of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally distinct cell clusters. Next, we established the developmental trajectories of epidermal cells, leaf mesophyll, and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell population in the vegetative apex, we created and applied a pipeline for interspecific single-cell expression data integration. We contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of primary vascular development between a model annual herbaceous and a woody perennial plant species. Our results offer a valuable resource for investigating the basic principles underlying cell division and differentiation conserved between herbaceous and perennial species, which also allows the evaluation of the divergencies at single-cell resolution. One Sentence SummarySingle-cell RNA-seq of the vegetative shoot apex resolved the genetic program of primary vascular development in hybrid poplar.

plant biology↗

bioRxiv2021

Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula

Rhizobia can establish symbiotic associations with legumes to provide plants with nitrogen needed in agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet the extent of chromatin changes and impact on gene expression is unknown. We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with rhizobia lipo-chitooligosaccharides. Using a novel approach, Dynamic Regulatory Module Networks, we predicted gene expression as a function of chromatin accessibility and accessible cis-regulatory elements. This approach identified the cis-regulatory elements and associated transcription factors that most significantly contribute to transcriptomic changes triggered by lipo-chitooligosaccharides. Regulators involved in auxin (IAA4-5,SHY2), ethylene (EIN3, ERF1) and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia. Significance StatementLegumes can fix nitrogen through symbiosis with rhizobia in root nodules, a critical mutualistic relationship for crop productivity and agricultural sustainability. Introducing this symbiotic relationship into non-legume crops is of great interest, but limited knowledge of host genome modifications induced by rhizobia has hampered such efforts. We applied time-course analysis of chromatin accessibility and gene expression of M. truncatula roots treated with rhizobia lipochitooligosaccharides. We show that extensive remodeling of genome accessibility drives a large component of the temporal transcriptome dynamics. By predicting gene expression as a function of accessibility of regulatory features, we identified known and novel regulators that are associated with early nodule development, which may be critical for its engineering into crops.

plant biology↗

bioRxiv2021

Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade

Nitrogen is one of the most inaccessible plant nutrients, but certain species have overcome this limitation by establishing symbiotic interactions with nitrogen-fixing bacteria in the root nodule. This root nodule symbiosis (RNS) is restricted to species within a single clade of angiosperms, suggesting a critical evolutionary event at the base of this clade, which has not yet been determined. While genes implicated in the RNS are present in most plant species (nodulating or not), gene sequence conservation alone does not imply functional conservation - developmental or phenotypic differences can arise from variation in the regulation of transcription. To identify putative regulatory sequences implicated in the evolution of RNS, we aligned the genomes of 25 species capable of nodulation. We detected 3,091 conserved noncoding sequences (CNS) in the nitrogen-fixing clade that are absent from outgroup species. Functional analysis revealed that chromatin accessibility of 452 CNS significantly correlates with the differential regulation of genes responding to lipo-chitooligosaccharides in Medicago truncatula. These included 38 CNS in proximity to 19 known genes involved in RNS. Five such regions are upstream of MtCRE1, Cytokinin Response Element 1, required to activate a suite of downstream transcription factors necessary for nodulation in M. truncatula. Genetic complementation of a Mtcre1 mutant showed a significant association between nodulation and the presence of these CNS, when they are driving the expression of a functional copy of MtCRE1. Conserved noncoding sequences, therefore, may be required for the regulation of genes controlling the root nodule symbiosis in M. truncatula.

plant biology↗

bioRxiv2021

Asc-Seurat - Analytical single-cell Seurat-based web application

SummarySingle-cell RNA sequencing (scRNA-seq) has become a popular approach for studying the transcriptome, providing a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data processing and uncover relevant biological information. We present Asc-Seurat, a feature rich workbench, providing a user-friendly and easy-to-install web application encapsulating the necessary tools for an all-encompassing and fluid scRNA-seq data analysis. Availability and implementationAsc-Seurat is available at https://github.com/KirstLab/asc_seurat/ and released under GNU 3 license. Contactmkirst@ufl.edu Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus

Single-cell transcriptome analysis has been extensively applied in humans and animal models to uncover gene expression heterogeneity between the different cell types of a tissue or an organ. It demonstrated its capability to discover the key regulatory elements that determine cell fate during developmental programs such as brain or heart development. Single-cell analysis requires the isolation and labeling of the messenger RNA (mRNA) derived from each cell. These challenges were primarily addressed in mammals by developing microfluidic-based approaches. For plant species whose cells contain cell walls, these approaches have generally required the generation of isolated protoplasts. Many plant tissues secondary cell wall hinders enzymatic digestion required for individual protoplast isolation, resulting in an unequal representation of cell types in a protoplast population. This limitation is especially critical for cell types located in the inner layers of a tissue or the inner tissues of an organ. Consequently, single-cell RNA sequencing (scRNA-seq) studies using microfluidic approaches in plants have mainly been restricted to Arabidopsis roots, for which well-established procedures of protoplast isolation are available. Here we present a simple alternative approach to generating high-quality protoplasts from plant tissue by characterizing the mRNA extracted from individual nuclei instead of whole cells. We developed the protocol using two different plant materials with varying cellular complexity levels and cell-wall structure, Populus shoot apices, and more lignified stems. Using the 10x Genomics Chromium technology, we show that this procedure results in intact mRNA isolation and limited leakage, with a broad representation of individual cell transcriptomes.

plant biology↗