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

Citation

Zluhan-Martínez, Estephania et al. (2022), Data for: Differentially expressed genes comparing WT plants vs xal1-2, Dryad, Dataset, https://doi.org/10.5061/dryad.cz8w9gj6n

Abstract

The balance between cell proliferation, differentiation, and elongation rates emerge from regulatory gene differentiation networks coupled to various signal transduction pathways, including those of reactive oxygen species (ROS). The Arabidopsis thaliana primary root has become a useful system to unravel such networks, as well as their interaction with signals that alter organ growth. The role of transcription factors, that regulate organ development, in mediating the role of ROS in root growth is just beginning to be studied. Here, we report that the MADS-box transcription factor XAANTAL1 (XAL1) mediates hydrogen peroxide (H2O2) role in primary root growth and it is involved in the morphogenesis of the columella stem cell differentiation in response to H2O2. Interestingly, our data suggest that XAL1 is a positive regulator of H2O2 concentration in the root meristem via regulating transcript accumulation of several peroxidases. Moreover, we found that XAL1 is necessary for the H2O2-induced inhibition of primary root growth through the negative regulation activities of the peroxidases and catalases. Furthermore, XAL1 and RETINOBLASTOMA-RELATED (RBR) are also necessary to positively regulate columella stem cell differentiation that is triggered by moderate H2O2 treatments. 

Methods

Three biological replicates of around 60 plants each were prepared, and the total RNA of 8-days-old roots was extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research, Irvine, USA) including a DNaseI treatment step to remove any contaminating DNA. The RNA’s integrity and quantity were checked using a 2100 Bioanalyzer, then it was sequenced by at the core facility of the Universidad Nacional Autónoma de México located at the Instituto de Biotecnología in Cuernavaca, Morelos, using an Illumina platform. For the differential expression analysis, raw sequencing data were trimmed with Trimmomatic version 0.39 (Bolger et al., 2014) using the parameters ILLUMINACLIP: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 HEADCROP:10. The quality of reads was evaluated with FastQC version 0.11.9 (Andrews, 2010) 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 used for differential expression analysis using DESeq2 (Love et al., 2014). Differentially expressed genes (DEGs) were identified with a p-adj.<0.05 and |log2FC|>1.

Usage Notes

The software required to open the data files is Excel.

Funding

UNAM-DGAPA-PAPIIT, Award: IN200920

Consejo Nacional de Ciencia y Tecnología, Award: 102959

UNAM-DGAPA-PAPIIT, Award: IN206220

UNAM-DGAPA-PAPIIT, Award: IN203220

UNAM-DGAPA-PAPIIT, Award: IN211721

Consejo Nacional de Ciencia y Tecnología, Award: 102987