Interpreting recently assembled genomes is biologically and computationally challenging. If new gene models have high sequence similarity with previously identified genes in model species, we assume similar functions for the new gene models until functional studies replace the current annotations. Through comparative genomics we try to identify the similarities and differences in the novel extremophyte genomes compared to model genomes with the prospect that the differences in the genome level hold the key to different adaptations observed at the phenome level of the extremophytes. We investigate select candidate genomic variation using transgenic  studies to confirm novel adaptive traits.