Plant resistance (R) genes played central roles in defense against invasive pathogens. In my study, R genes of two major families, NBS-LRR and LRR-Pkinase, were identified in genomes of plant species ranging from algae to angiosperm followed by phylogenetic analysis to investigate their origin and early evolution, which was summarized in a hypothesized evolutionary model. Further, an original pipeline was developed to detect R gene insertions (RGI) in the population of three cultivated crop species (S.bicolor, Z.mays and O.sativa), the result of which provided the insights into the recent evolution of R gene at a finer scale for the first time. In addition, novel RGI loci originated after divergence with close wild relative and fully fixed in the cultivated populations were identified for their tremendous value to guide downstream functional genomics studies. As a result, R gene studies based on larger and finer evolutionary scales together helped to gain more comprehensive understanding of their evolution in plant genomes. Second, to investigate structural variation (SV) in crops species, SVs were detected in the populations of the three crop species followed by population genetics analysis. Both population-specific and across-population patterns were identified and analyzed. Further, to investigate the temporal dynamics of genome rearrangement (GR) events that resulted in observed SV loci, an original pipeline was implemented that integrates information in regional phylogeny and detected SV loci to infer the occurrence time of underlying GR events. Waves of GR events were unraveled during the domestication history for the first time. In addition, comprehensive tree distance analysis was performed which reveals complex patterns of phylogenetic heterogeneity across genome both within and between taxa. Last, to accommodate with the fast-growing trend towards the research mode involving multiple data types and formats, a framework, named visframe, was proposed for a generic, integrative and highly customizable data processing and visualization tool, under the guide of which the core visframe package was implemented. Further, a standalone GUI, named visframeUI, was implemented based on the core visframe package as the demonstration of the proposed framework.