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Molecular Approaches to Elucidating Adaptation to Serpentine Soils Using the Caulanthus amplexicaulis Complex (Brassicaceae)
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Serpentine endemic plants are excellent models for the study of molecular evolution as they provide extreme examples of adaptation to environment. Serpentine outcrops are derived from ultramafic rock and have low levels of essential plant nutrients (e.g., N, P, K, Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, Co), very poor moisture availability, high levels of light, and elevated soil temperatures. These outcrops provide habitat to the endemic plant species, Caulanthus amplexicaulis var. barbarae (CAB). Its sister species, C. amplexicaulis var. amplexicaulis (CAA), is found predominately on granite soils and is intolerant to serpentine soils. Comprehensive reference transcriptomes of CAA and CAB were assembled and annotated for use in protein coding gene comparisons. Orthologs between CAA and CAB reveal high genome-wide dN/dS ratios and result from the composite effects of drift, positive selection, and the relaxation of negative selection. Also, paralogs within each taxon revealed two periods of elevated gene duplication. Further, distribution of dS is strongly bimodal indicating two distinct divergence events between the taxa, and suggesting that introgression may have contributed to serpentine adaptation. Common-garden and reciprocal transplant experiments were performed on natural granite and serpentine soils using CAA and CAB. RNA-seq analyses were implemented to calculate global expression patterns and identify differentially regulated genes that may play a role in serpentine adaptation. Initial efforts were implemented to answer the following three questions: which genes are constitutively expressed in CAB, which genes are induced in CAB on serpentine outcrops, and which genes are induced in CAA on serpentine outcrops? RNA-seq data implicates a suite of chloroplast and plastids related genes being constitutively expressed in CAB; this is an unexpected and novel finding. Genes induced in CAB on serpentine outcrops include those with roles in nutrient acquisition and transport and heavy metal binding. Genes induced in CAA on serpentine outcrops indicate response to nutrient starvation and galactose binding/transport. Ultimately results from these analyses, in conjunction with QTL mapping and population genetic data, will be used to find high quality candidate genes that confer tolerance to serpentine soils.
Hawkins, Angela Krista (2018). Molecular Approaches to Elucidating Adaptation to Serpentine Soils Using the Caulanthus amplexicaulis Complex (Brassicaceae). Doctoral dissertation, Texas A & M University. Available electronically from