Project description: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).
Project description:Cellulose from plant biomass is the largest renewable energy resource of carbon fixed from the atmosphere, which can be converted into fermentable sugars for production into ethanol. However, the cellulose present as lignocellulosic biomass is embedded in a hemicellulose and lignin matrix from which it needs to be extracted for efficient processing. Here, we show that expression of an Arabidopsis transcription factor SHINE (SHN) in rice, a model for the grasses, causes a 34% increase in cellulose and a 45% reduction in lignin content. Rice genotypes expressing the Arabidopsis SHN2 gene hereafter called rice AtSHN lines were used in this study. Progenies of three independent AtSHN lines were grown in controlled growth chambers. For all analyses, six plants were used for each of the two transgenic lines and WT. For total RNA isolation, rice leaf tissue of WT and AtSHN lines was used. Samples were hybridized to the rice Affymetrix GeneChip.
Project description:Our previous studies, comparing russeted vs. waxy apple skin, highlighted a MYeloBlastosys (Myb) transcription factor (MdMYB52-like), which displayed a correlation with genes associated to the suberization process. The present article aims to assess its role and function in the suberization process. Phylogenetic analyses and research against Arabidopsis thaliana MYBs database were first performed and the tissue specific expression of MdMYB52-like was investigated using RT-qPCR. The function of MdMYB52-like was further investigated using Agrobacterium-mediated transient overexpression in Nicotiana benthamiana leaves. An RNA-Seq analysis was performed to highlight differentially regulated genes in response MdMYB52-like. Transcriptomic data were supported by analytical chemistry and microscopy. A massive decreased expression of photosynthetic and primary metabolism pathways was observed with a concomitant increased expression of genes associated with phenylpropanoid and lignin biosynthesis, cell wall modification and senescence. Interestingly key genes involved in the synthesis of suberin phenolic components were observed. The analytical chemistry displayed a strong increase in the lignin content in the cell walls during MdMYB52 expression. More specifically, an enrichment in G-Unit lignin residues was observed, supporting transcriptomic data as well as previous work describing the suberin phenolic domain as a G-unit enriched lignin-like polymer. The time-course qPCR analysis revealed that the observed stress response, might be explain by this lignin biosynthesis and by a possible programmed senescence triggered by MdMYB52-like. The present work supports a crucial regulatory role for MdMYB52 in the biosynthesis of the suberin phenolic domain and possibly in the fate of suberized cells in russeted apple skins.