Abstract
Abstract Plants grow in close associations with fungi—pathogens, symbionts, and endophytes—and depend on these associations for success. Therefore, understanding the mechanisms of these interactions is important in order to create optimal conditions for plant growth. Genomics is a powerful tool not only to discover the potential encoded in genomes of both plants and plant-associated fungi but also to monitor dynamics of their interactions through gene expression and other genome-enabled analyses. Next-generation sequencing technologies offer tools to explore nature's wide array of plant–fungal interactions in unprecedented depth, and the sheer volume of data produced is enormous. Several approaches to assemble, annotate, and analyse this wealth of genomics data are discussed in this chapter.
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