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

BACKGROUND: Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions, and translation. However, plant genomes have not been assessed for the presence of these structure-altering polymorphisms or "riboSNitches." RESULTS: We 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 also associated with differences in the abundance of their respective transcripts, implying a role in regulating the gene's expression in adaptation to local climate conditions. We then computationally predict riboSNitches transcriptome-wide in mRNAs of 879 naturally inbred Arabidopsis accessions. We characterize correlations between SNPs/riboSNitches in these accessions and 434 climate descriptors of their local environments, suggesting a role of these variants in local adaptation. We integrate this information in CLIMtools V2.0 and provide a new web resource, T-CLIM, that reveals associations between transcript abundance variation and local environmental variation. CONCLUSION: We functionally validate two plant riboSNitches and, for the first time, demonstrate riboSNitch conditionality 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 greatly facilitate in silico studies of natural genetic variation, its phenotypic consequences, and its role in local adaptation

The stable isotope ecology of terrestrial plant succession

We review the relevance and use of stable isotopes for the study of plant community succession. Stable isotope measurements provide information on the origin of resources acquired by plants, the processes governing resource uptake and transformation, and the physiological and environmental conditions of plant growth. When combined with measurements of the stable isotope ratio values of soil microbial biomass, soil organic matter and plant litter, isotope measurements of plants can indicate effects of successional changes on ecosystem processes. However, their application to questions of plant succession and ecosystem change is limited by the degree to which the underlying assumptions are met in each study, and complementary measures may be required, depending upon the question of interest. First, we discuss the changes that occur in the stable isotope composition of plants and ecosystems with ontogeny and species replacements, as well as their potential evolutionary significance. Second, we discuss the imprints of plant competition and facilitation on leaf and wood tissue, as well as how stable isotopes can provide novel insights on the mechanisms underlying plant interactions. Finally, we discuss the capacity for stable isotope measurements to serve as a proxy record for past disturbances such as fire, logging and cyclones

The stable isotope ecology of terrestrial plant succession

We review the relevance and use of stable isotopes for the study of plant community succession. Stable isotope measurements provide information on the origin of resources acquired by plants, the processes governing resource uptake and transformation, and the physiological and environmental conditions of plant growth. When combined with measurements of the stable isotope ratio values of soil microbial biomass, soil organic matter and plant litter, isotope measurements of plants can indicate effects of successional changes on ecosystem processes. However, their application to questions of plant succession and ecosystem change is limited by the degree to which the underlying assumptions are met in each study, and complementary measures may be required, depending upon the question of interest. First, we discuss the changes that occur in the stable isotope composition of plants and ecosystems with ontogeny and species replacements, as well as their potential evolutionary significance. Second, we discuss the imprints of plant competition and facilitation on leaf and wood tissue, as well as how stable isotopes can provide novel insights on the mechanisms underlying plant interactions. Finally, we discuss the capacity for stable isotope measurements to serve as a proxy record for past disturbances such as fire, logging and cyclones