Gene expression differs in codominant prairie grasses under drought

Grasslands of the Central US are expected to experience severe droughts and other climate extremes in the future, yet we know little about how these grasses will respond in terms of gene expression. We compared gene expression in Andropogon gerardii and Sorghastrum nutans, two closely related co-dominant C4 grasses responsible for the majority of ecosystem function, using RNA-seq. We compared Trinity assemblies within each species to determine annotated functions of transcripts responding to drought. Subsequently, we compared homologous annotated gene-groups across the two species using cross-species meta-level analysis and functional clustering based on key terms. The majority of variation was found between species, as opposed to between drought and watered treatments. However, there is evidence for differential responses; Andropogon allocated gene expression differently compared to Sorghastrum, suggesting Andropogon focuses on stress alleviation (such as oxygen radical scavenging) rat...,

raw_data
Contains raw sequence data.

Trinity_andropogon_02122016.fasta

Trinity assembly of the Andropogon gerardii transcriptome, assembled Feb 12, 2016.

File: Trinity_andro_out.Trinity.02122016.fasta

Trinity_sorghastrum_04102016.fasta

Trinity assembly of Sorghastrum nutans transcriptome, assembled Apr 10, 2016.

File: Trinity_sorgh_out.Trinity.fasta

RSEM_read_counts
Raw and TMM-normalized read counts for transcript expression prior to analysis.

edgeR_results_andropogon
Counts and differential expression for Andropogon.

edgeR_results_both_species
Preliminary count data for annotation clustered genes compared between the two species. This information was processed further in the pipeline to account for multiple copy numbers (orthologs, paralogs)

edgeR_results_sorghastrum
Count and differential expression data for Sorghastrum.

Kristiansson_analysis_results
Accounts for multiple different gene copy numbers in differential expression.

all_paralogs_bothspecies

Count...,