Data for: The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype

Through developmental plasticity, an individual organism integrates influences from its immediate environment with those due to the environment of its parents. While both effects on phenotypes are well documented, their relative impact has been little studied in natural systems, especially at the level of gene expression. We examined this issue in four genotypes of the annual plant Persicaria maculosa by varying two key resources light and soil moisture in both generations. Transcriptomic analyses showed that the relative effects of parent and offspring environment on gene expression (i.e., the number of differentially expressed transcripts, DETs) varied both for the two types of resource stress and among genotypes. For light, immediate environment induced more DETs than parental environment for all genotypes (although the precise proportion of parental versus immediate DETs varied among genotypes). By contrast, the relative effect of soil moisture varied dramatically among genotypes, f..., Parental and offspring generations
We studied 4 genetic lines of Persicaria maculosa, an annual generalist plant of allotetraploid origin (Kim et al., 2008). Achenes from each of four experimental genotypes (MHF1, NAT1, NAT2, and TP2) were grown to reproductive maturity in one of three randomly assigned greenhouse treatments: full sun with moist soil (“High Light/Moist”), full sun with dry soil (“Dry”), or simulated shade with moist soil (“Shade”). Note that the parental High Light/Moisture treatment provided a stress-free (“control”) comparison for both the parental Dry and the parental Shade treatments.
Mature achenes from one (self-fertilized) parent plant for each genotype × Parent treatment combination were germinated on petri plates and transplanted into pots (3 replicate seedings per pot). Experimental pots (4 genotypes × 5 [Parent treatment × Offspring treatment] combinations × 3 replicates = 60 pots) were raised in a randomized complete block design in a Conviron E2 growth cham..., , # The Relative Impact of Parental and Current Environment on Plant Transcriptomes Depends on Type of Stress and Genotype

# Earley, Feiner, Alvarez, Coolon, and Sultan

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Experimental data and code for Earley et al. \"The Relative Impact of Parental and Current Environment on Plant Transcriptomes Depends on Type of Stress and Genotype.\" Please refer to this manuscript for detailed methodology used to generate this data.

## Description of the data and file structure

The data in this repository pertain to the differential expression analysis of RNA-seq data. The data folder contains all necessary sample information and outputs for the differential expression analysis. The sub-folder Counts contains kallisto quant outputs, data quantifying the abundance of each transcript in each sample. The sub-folder GO within data contains all all output files for the gene ontology analysis. The sub-folder venn-diagrams within data contains all output files for the Venn diagram visualization and ove...