Project description:Transcriptomic analysis was performed on the main inflorescence stems of wild-type and lignin-modified lines growing under the same conditions.
Project description:af09_lignin - stem developement - Transcriptome analysis of lignin mutants and UV stress effect on secondary wall synthesis - transcription frofiling of stem developement in Arabidopsis thaliana. time course with 3 points: 2cm, 10 cm and 25cm (maturation) Keywords: time course
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:af09_lignin - dml6 - Transcriptome analysis of lignin mutants and UV stress effect on secondary wall synthesis - DML6 vs S DML6+UV vs S+UV S vs S+UV DML6 vs DML6+UV Keywords: normal vs disease comparison,treated vs untreated comparison
Project description:Inflorescence stems of 20 Arabidopsis thaliana mutants, each mutated in a single gene of the lignin biosynthetic pathway (PAL1 , PAL2, C4H, 4CL1, 4CL2, CCoAOMT1, CCR1, F5H1, COMT and CAD6, two mutant alleles each) were analyzed by microarrays.
Project description:ngs2018_05_tor-analysis of arabidopsis mutants tor/lst8/yak1/maktor-Analysis of Arabidopsis insertion and suppressor mutants linked to the TOR signaling pathway.-Comparison of in vitro grown plantlets for lst8, yak1 mutants and double mutants corresponding to suppressor lines. Comparison of in vitro grown plantlets for mutants affected in LST8 interacting proteins (MAKTOR) compared to wild type.
Project description:This switchgrass project aims to identify metabolic consequences of lignin manipulation and impact on the responses to drought stress in switchgrass. Here we examine elongating internodes of six switchgrass lignin biosynthesis-altered transgenic and mutant and their isogenic wild-type negative segregant lines. Studies in the eudicot, Arabidopsis, have revealed metabolic and transcriptional differences in lignin biosynthesis mutants that appear to relate to feedback mechanisms for plants to compensate for lignin pathway disruption. Specifically, disruption of core lignin biosynthesis gene expression leads to increases in expression of cell wall-related pathways; whereas, disruption of downstream S- and G-lignin specific genes leads to down-regulation of lignin biosynthesis. This experiment allows us to test the generality of this observation in a bioenergy-relevant species. While we generally expect the same patterns, progress revealing differences in grass lignin biosynthesis pathways relative to eudicots suggests that we might also uncover differences.
The work (proposal:https://doi.org/10.46936/10.25585/60000468) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.