biostudies-arrayexpressMatteo ButiMimosa pudicahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14230Priming is a mechanism used by plants to rapidly respond to external stimuli, becoming essential for their survival and resistance to unfavorable conditions. The physiological state acquired by a plant after the exposure to repeated stress is the result of molecular mechanisms determining plant’s memory of past stress events. Mimosa pudica is a plant known for its ability to respond to physical disturbance by folding its leaves. The movement is determined by a strong Ca2+ influx, which acts as both osmotic pressure regulator and secondary messenger for gene expression. Considering the need to intervene in a sustainable way to counteract the ever-increasing biotic and abiotic stresses caused by climate change, it would be particularly interesting to deepen our knowledge on stress tolerance development in primed plants. From this perspective, M. pudica can be a valuable model for studying the molecular mechanisms related to adaptive memory acquisition after repeated stress events. In this study, the gene regulatory networks underlying M. pudica leaf closure following single and multiple mechanical disturbances (droppings) were investigated.biostudies-arrayexpressSample Collection - Leaves of non-stimulated, stimulated and over-stimulated plants were cut at the base of the hypocotyls and immediately snap frozen in liquid nitrogen.Growth Protocol - Plants at identical developmental stages (young, 10 cm tall, 5 leaves brunches) were purchased from a local specialized nursery and grown for a week for acclimatation in a growth chamber using controlled conditions of light, temperature (23 °C) and humidity.Sample Treatment - Three different stimulations were applied to plants, and samples were collected immediately after the treatments described below. 1. Non stimulated plants: untreated plants, with leaves wide open. The leaves were cut at the base of the hypocotyls and immediately snap frozen in liquid nitrogen (these samples were named C) 2. Stimulated plants: plants were subjected to a single a sudden drop from the height of 10 cm. Closed leaves were cut at the base of the hypocotyls and immediately snap frozen in liquid nitrogen (these samples were named T) 3. Overstimulated plants: plants were subjected to repetitive drops from the height of 10 cm, waiting for cycles of closing and reopening of leaves until they did not close/respond to the movement anymore (adaptation). Still open leaves were cut at the base of the hypocotyls and immediately snap frozen in liquid nitrogen (these samples were named M).Nucleic Acid Extraction - Total RNA was extracted from samples of Mimosa leaves of plants in control conditions (C) (no external stimuli), of plants after one drop (T), and after several drops until habituation (M), collected as previously reported. For each experimental conditions, three biological replicates were carried out. Samples were immediately frozen in liquid nitrogen and stored at −80 °C. RNA extraction was performed using 100 mg of frozen material ground with a pestle and mortar in liquid nitrogen using the Norgen's Plant/Fungi Total RNA Purification Kit RNA. Final elutions were performed using 60 μL of RNase-free water. RNA was treated with DNAase before quantification. RNA quality was determined using the Agilent 2100 Bioanalyzer System (RNA 6000 nano kit - Biorad Inc.)Library Construction - Sequencing libraries were obtained following the procedure of Truseq Stranded mRNA Library Prep (Illumina) and using Truseq RNA Single Indexes (3 libraries for each of the three experimental conditions). The concentration of each library was determined using Qubit™ 4 Fluorometer (dsDNA High Sensitivity Kit - Invitrogen).Sequencing - Sequencing was performed using Novaseq 6000 SP Reagent Kit (100 cycles). Samples were run in a single flow cell.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - After RNA-Seq raw reads quality was assessed with FastQC v0.11.5, adapters sequences and low-quality reads were removed with Trimmomatic v0.39. The filtered RNA reads of all the sequenced libraries were used for a de novo transcriptome assembling with Trinity v2.13.2, and assembled transcripts were clustered using CD-hit v4.8.1 with default parameters to produce a set of ‘non-redundant’ representative transcripts. The filtered RNA reads of the sequenced libraries were mapped back to the final Mimosa transcriptome using Bowtie2 v2.4.4 with default parameters, while the expression quantification of each transcript was carried out with the ‘quant’ and ‘quantmerge’ tools of Salmon v1.4.Data Transformation - EdgeR package was used to filter out unexpressed or poorly expressed transcripts (a transcript was considered to be ‘active’ if the reads per million mapping to that gene were >1 in at least two libraries), to normalize the RNA libraries depending on their dimension and assigning a CPM value for each active transcript and for each RNA library.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMimosa pudicaMatteo ButifalseThe transcriptional mechanism behind Mimosa pudica leaf-folding in response to physical disturbancePriming is a mechanism used by plants to rapidly respond to external stimuli, becoming essential for their survival and resistance to unfavorable conditions. The physiological state acquired by a plant after the exposure to repeated stress is the result of molecular mechanisms determining plant’s memory of past stress events. Mimosa pudica is a plant known for its ability to respond to physical disturbance by folding its leaves. The movement is determined by a strong Ca2+ influx, which acts as both osmotic pressure regulator and secondary messenger for gene expression. Considering the need to intervene in a sustainable way to counteract the ever-increasing biotic and abiotic stresses caused by climate change, it would be particularly interesting to deepen our knowledge on stress tolerance development in primed plants. From this perspective, M. pudica can be a valuable model for studying the molecular mechanisms related to adaptive memory acquisition after repeated stress events. In this study, the gene regulatory networks underlying M. pudica leaf closure following single and multiple mechanical disturbances (droppings) were investigated.2025-09-21T00:00:00Z2025-09-21T06:07:26.797Z2024-07-08T16:40:48.352ZE-MTAB-14230ERP161835EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969