Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Dawn anticipation

ABSTRACT: To investigate the role of TIC in the morning perception process, we performed a transcriptome analysis of the wild type and time for coffee mutant (tic-2) at dawn. An additional file is included. In this file, the expression values for the replicates are condensed in a single data point obtaining one mean and standard deviation of the expression values per genotype. The protocol for this file is: log2 fold change followed by a False Discovery Rate with a p-value equal or below 0.05.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: alfredosvwm@yahoo.com.mx Sanchez-Villarreal

PROVIDER: E-MTAB-1362 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

TIME FOR COFFEE is an essential component in the maintenance of metabolic homeostasis in Arabidopsis thaliana.

Sanchez-Villarreal Alfredo A Shin Jieun J Bujdoso Nora N Obata Toshihiro T Neumann Ulla U Du Shen-Xiu SX Ding Zhaojun Z Davis Amanda M AM Shindo Takayuki T Schmelzer Elmon E Sulpice Ronan R Nunes-Nesi Adriano A Stitt Mark M Fernie Alisdair R AR Davis Seth J SJ

The Plant journal : for cell and molecular biology 20130823 2

Plants often respond to environmental changes by reprogramming metabolic and stress-associated pathways. Homeostatic integration of signaling is a central requirement for ensuring metabolic stability in living organisms. Under diurnal conditions, properly timed rhythmic metabolism provides fitness benefits to plants. TIME FOR COFFEE (TIC) is a circadian regulator known to be involved in clock resetting at dawn. Here we explored the mechanism of influence of TIC in plant growth and development, a ...[more]

PMID: 23869666

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Project description:Purpose: Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq) to identify the candidate genes and alleles and to explore the evolutionary signatures of selection Methods: We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. We used reference-guided transcriptome mapping to study gene expression. Reads mapping to predicted transcripts were analysed with edgeR pacakge to study differntial expression of genes under control and water-stress conditions. SNPs within the genes were obtained using pileup file generated with samtools and the SNP frequencies were analysed with VarScan package. SNPs were further characterised as sysnonymous and non-synonymous using popoolation2 pacakge. Results: Several genes showed differential expression between control and stress conditions. Gene ontology (GO) enrichment tests revealed up-regulation of 140 stress-related gene categories and down-regulation of 35 metabolic and cell wall organisation gene categories. More than 190,000 single nucleotide polymorphisms (SNPs) were detected and 2737 of these showed differential allelic expression. Allelic expression of 52% of these variants was correlated with total gene expression. Signatures of selection patterns were studied by estimating the proportion of nonsynonymous to synonymous substitution rates (Ka/Ks). The average Ka/Ks ratio among the 13,719 genes was 0.39 indicating that most of the genes are under purifying selection. Among the positively selected genes (Ka/Ks > 1.5) apoptosis and cell death categories were enriched. Of the positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments. Conclusions: Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants. Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study. Leaf mRNA of 12 samples were used to study the gene expression under control and water-stress conditions. Three samples under water-stress conditions and three samples under control conditions were used as biological replicates for differenctial gene expression between the treatments. High-throughput sequence reads from mRNA samples were generated by deep sequencing with Illumina GAIIx.

Dataset Information

Dawn anticipation

Publications

TIME FOR COFFEE is an essential component in the maintenance of metabolic homeostasis in Arabidopsis thaliana.

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