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Understanding how organisms can respond at different time scales is an essential component of deciphering the impact and long-term consequences of global change. Genomics tools can provide information on the molecular mechanisms underlying response in a broad array of wild organisms and biologically relevant conditions. Further, we now know that non-genetic effects can result in heritable, novel phenotypes even without variation in DNA sequence and could therefore provide an unappreciated source of response. We use reduced a variety of sequencing approaches to explore the potential role of genetic and epigenetic processes in natural and controlled studies of the invasive Japanese knotweed. We use resources developed in model plant species research to inform our findings in these invasive plants. Combined, our studies will enhance our understanding of how plants respond to environment on different time scales, and become invasive.