Systems approaches to understanding plant extremophile lifestyles

Plants evolutionarily adapted to thrive in highly stressful environments – extremophiles - have traditionally been studied under ecological objectives. As one result of applying next-generation sequencing tools genomes and transcriptomes of several extremophile species have now become available.  Clearly, the extreme habitats to which these species became adapted left traces in their genomes.  Gene duplications and retention of duplicates that support extremophile life abound.  Neo-functionalization in terms of expression control and protein activity is documented, suggesting problems for systems integration. Foremost is the concern that gene expression networks established for a few species will require modifications to account for gene content and neo-functionalization of genes  with respect to transcription control and protein function. With respect to specific environmental adaptations significant differences in gene and protein control can be expected.  Another aspect is the detection of a fraction of extremophile genomes/transcriptomes encoding novel, genus- and species-specific, functions.  Another topic requiring attention is insecurity in annotation and identification of genes described in model species.  Homology constitutes only a limited descriptor of function.  We will compare genomes/ transcriptomes of extremophiles in genus Thellungiella with those of relatives in genus Arabidopsis.  Such a systems-oriented approach will foster modeling dynamic changes to genetic networks that accompany the adaptation to extreme stress conditions.