Data from: Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis

BackgroundGenome-Wide Association Studies (GWAS) aim to correlate
phenotypic changes with genotypic variation. Single nucleotide variants
(SNVs) within transcripts may alter mRNA structure, with potential impacts
on transcript stability, macromolecular interactions and translation.
However, no plant genomes have been yet assessed for the presence of these
structure-altering polymorphisms or “riboSNitches”.ResultsWe
experimentally demonstrate the presence of riboSNitches in transcripts of
two Arabidopsis genes, ZINC RIBBON 3 (ZR3) and COTTON GOLGI-RELATED 3
(CGR3), which are associated with continentality and temperature variation
in the natural environment. These riboSNitches are associated with
differences in the abundance of their respective transcripts, implying
their role in regulating gene expression in adaptation to local climate
conditions. We computationally predict transcriptome-wide riboSNitches in
879 naturally inbred Arabidopsis accessions. We also characterize
correlations between SNPs/riboSNitches in these accessions and 434 climate
descriptors of local environments; suggesting the role of these variants
in local adaptation. We integrate this information in CLIMtools V2.0 and
provide a new web resource, T-CLIM, which allows users to determine the
association of transcript abundance variation with climate
variation.ConclusionsWe functionally validate two plant riboSNitches and,
for the first time, demonstrate riboSNitch is conditionally dependent on
temperature, coining the term conditional riboSNitch. We provide the first
pan-genome wide prediction of riboSNitches in plants. We expand our
previous CLIMtools web resource with riboSNitch information and with 1868
additional Arabidopsis genomes and 269 additional climate conditions,
which will facilitate in silico studies of natural genetic variation, its
phenotypic consequences and its role in local adaptation.