| Summary: | <p>Reliable, high-throughput and low-cost next-generation sequencing technologies have invigorated genetic research into non-model organisms over the last decade. In this work, RNA-Seq was employed to obtain the first-ever transcriptomes of two groups of closely related plant taxa possessing distinctive complex physiological traits, namely metal hyperaccumulation and C<sub>4</sub> photosynthesis.</p> <p>Metal hyperaccumulator plants possess an extraordinary ability to take up trace elements from the soil and accumulate them to high concentrations in their shoots, probably to serve as a type of elemental defence against natural enemies. Taxonomically, the most common form of metal hyperaccumulation, nickel hyperaccumulation, is encountered on nickel-rich ultramafic (serpentine) soils, and is found with the highest frequency (ca. 51 species) in the genus <em>Alyssum</em> (family Brassicaceae). Here, the genetic basis and evolutionary history of nickel tolerance and hyperaccumulation was investigated in the <em>Alyssum serpyllifolium</em> Desf. species complex, which contains both serpentine and non-serpentine populations of unresolved phylogenetic relationships on the Iberian Peninsula. Genome scans for outlier loci and differential expression analyses identified a number of candidate hyperaccumulator genes common to two serpentine populations found in Portugal and Spain, but the majority of adaptive variation was of local origin. Phylogenetic and population-genetic inferences based on neutral and putatively adaptive loci suggested that the key genes for the nickel hyperaccumulation trait evolved once and spread across serpentine populations early in the history of this species, with no genetic isolation but continued recent gene flow between serpentine and non-serpentine populations.</p> <p>To test the power of next-generation sequencing for analysing the genetic basis of a separate complex trait, a cross-species comparison was performed using RNA-Seq of two congeneric tropical species, the C<sub>4</sub> plant Alternanthera pungens Kunth and the C<sub>3</sub> plant Alternanthera philoxeroides (Mart.) Griseb. f. <sub>angustifolia</sub> Suess. (family Amaranthaceae). These species were cultivated at two different temperatures and showed significant differences in levels of overall gene expression plasticity and isoform switching in certain photosynthesis genes, which it is proposed may explain the observed difference in the ability of these two species to acclimate to low and high growth temperatures.</p>
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