Gene expression profiling of lignin biosynthetic mutants of Arabidopsis

Purpose: To investigate the global impact of lignin perturbation on transcription in plants, we analyzed transcriptomes from rapidly lignifying stem tissue in wild-type Arabidopsis and 13 selected mutants. Methods: RNA-sequencing was conducted to profile the transcriptome in basal stem tissue of Arabidopsis plants. PolyA+ RNA libraries were constructed and paired-end sequencing was performed on Illumina NovaSeq 6000. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using HISAT2. Gene counts were analyzed using HTSeq-count program and differential gene expression using DESeq2. Results: The whole dataset contains 20974 expressed genes and 5581 differentially expressed genes in at least one mutant (ANOVA, FDR < 0.05, Fold change = 2 fold). Overall design: Gene expression profiles of 8 biological replicates of wild type and 4 biological replicates of 13 mutants with perturbed lignification were generated from inflorescence stem tissue of 28-day-old Arabidopsis by RNA-sequencing.