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Plants are the primary producers for all different types of ecosystems on earth. They use abiotic sources of energy such as light and inorganic chemical compounds to build organic molecules which are used as carbon and energy source by all other organisms. Evolutionary biologists have long considered plant domestication by humans as a coevolutionary process between plants and human beings in which both the partners have changed over time. However, there are other important factors that seem to have been ignored while discussing the “plant-hominin coevolutionary continuum.” These are the different environmental conditions including various biotic and abiotic factors that have changed so much over time. These changes range from fast, short-term, or acute to slow, gradual, long-term, or chronic changes. Plants that adapted to these changing environmental conditions were favored by humans for domestication and hence they exist today, whereas those that could not cope with environmental changes went extinct. The genetic record of such adaptations is carried by today’s plant genomes. These adaptations are the genetic legacy of hundreds of millions of years of natural selection shaped by the changing environment. Though plants affect the environment, they are shaped by the environment. Humans have recently woken up to their self-made problems of overpopulation, urbanization, pollution, indiscriminate use of fossil fuels, rising temperatures, melting glaciers, and others. All these ultimately translate into climate change. Though climate change events have been recorded throughout the history of the planet earth, every time life found a way to survive. But this time the situation is much worse as climate is changing at a much faster and severe rate and scientists predict that it may be impossible for the earth, humans, plants, and others to survive. In this scenario being the only primary producers, plants are as equally an important stakeholder as humans. If planet earth is to support the predicted nine billion human population by 2050, crop plants will need to tolerate and adapt to climate change at a rate and way that they have never done before. How plants sense different stresses and adapt to adverse environmental conditions are fundamental questions that need to be answered. In this chapter, we gather the important scientific studies that try to answer these questions through research, experimentation, and evidence at molecular level. We have discussed plant adaptation to adverse environment via strategies like calcium signaling, MAP kinase signaling, stress-sensing and other signaling molecules, antioxidant defense, phytohormone biosynthesis and signaling, transcriptional regulation of response cascades under stress, and the cross talk between different stress responses.

The implementation of a pan-genomic framework initiated with the realization that the genome of every strain of a species is unique. Previously, the reference genome was used to describe a species. Pan-genome can be categorized into three ways including core genes that are present in every sequenced strain, variable, or dispensable genes that are common in some strains and unique genes found in just one strain, offering an enormous panel of usages. Numerous bioinformatics tools have been exploited for pan-genomic analysis which may help to define species. By classifying all the genomic data, it may be possible to redefine species and sort them according to their genomic content. These studies have become nearly necessary for bacterial genome comparisons and are also employed in analyzing the genomic content of other plant pathogens. Pathogens including bacteria and fungi offer an exceptional opportunity for pan-genome assembly as the size of their genomes is comparatively small. Similarly, the classification is dependent on the nature of pan-genome (open or closed) as well as the lifestyle of the species. Pan-genomic analyses have gated the ways for researchers to develop universal vaccines since last decade that might provide protection against all strains in a species or even against several related species. Since this approach has a potential for organizing pathogenic diversity, integrating pan-genomics with phylogeny, and phylogenomics will be an interesting viewpoint for the future.