Data for: Differentially expressed genes comparing WT plants vs xal1-2

The balance between cell growth, proliferation, and differentiation rates emerges from gene regulatory networks coupled to various signal transduction pathways, including reactive oxygen species (ROS) and transcription factors (FTs), enabling developmental responses to environmental cues. The Arabidopsis thaliana's primary root has become a valuable system for unraveling such networks. Recently, the role of transcription factors mediating ROS's inhibition of primary root growth has begun to be characterized. This study demonstrates that the MADS-box transcription factor XAANTAL1 (XAL1) is an essential regulator of hydrogen peroxide (H2O2) in primary root growth and root stem cell niche identity. Interestingly, our findings suggest that XAL1 acts as a positive regulator of H2O2 concentration in the root meristem by directly regulating genes involved in oxidative stress response, such as PEROXIDASE 28 (PER28). Moreover, we found that XAL1 is necessary for the H2O2-induced inhibition of primary root growth through the negative regulation of peroxidase and catalase activities. Furthermore, we found that XAL1, in conjunction with RETINOBLASTOMA-RELATED (RBR), is essential for positively regulating the differentiation of columella stem cells in response to moderate oxidative stress induced by H2O2 treatment.

Methods
Three biological replicates, each consisting of approximately 60 plants, were prepared. The total RNA from 8dps roots was extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research, Irvine, USA), including a DNaseI treatment step to remove contaminating DNA. The RNA integrity and quantity were assessed using a 2100 Bioanalyzer. Subsequently, the RNA was sequenced at the “Unidad de Síntesis y Secuenciación de DNA” of the Universidad Nacional Autónoma de México located at the Instituto de Biotecnología in Cuernavaca, Morelos, using an Illumina platform. For the analysis of differential transcript accumulation analysis, the raw sequencing data underwent trimming with Trimmomatic version 0.39 (Bolger et al., 2014) using the following parameters: ILLUMINACLIP: 2:30:10 LEADING:3 TRAILING:3 SLIDING WINDOW:4:15 MINLEN:50 HEADCROP:10. The quality of reads was evaluated with FastQC version 0.11.9 (Andrews, 2010) both before and after the trimming process. Biological replicates were aligned to the Arabidopsis genome from TAIR10 (https://www.arabidopsis.org/) and the abundance of the transcripts was estimated using Subread version 2.0.1 (Liao et al., 2019). Raw count tables were employed for differential transcript accumulation analysis using DESeq2 (Love et al., 2014). Differentially expressed genes (DEGs) were identified with an adjusted p-value (padj) <0.05 and log2 fold change > 1.5 (Table S5). Gene Ontology (GO) enrichment analysis was conducted with agriGO v2.0 (http://systemsbiology.cau.edu.cn/agriGOv2/).