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Karyotypic evolution is a prominent feature in the diversification of many plants and animals, yet the role that chromosomal changes play in the process of diversification is still debated. At the diploid level, chromosome fission and/or fusion are necessary components of chromosomal structural change associated with diversification. Yet the genomic features required for these events remain unknown. Here we present an overview of what is known about genomic structure in Cyperales, with particular focus on the current level of understanding of chromosome number and genome size and their impact in a phylogenetic context. We outline ongoing projects exploring genomic structure in the order using modern genomics techniques coupled with traditional data sets. Additionally, we explore the questions to which this approach might be best applied, and in particular, detail a project exploring the nature of genomic structural change at the diploid level in genus Carex, a group in which chromosome fission/fusion events are common and associated with diversification of many of its 2000 species. A hypothesized mechanism for chromosome number change in this genus is agmatoploidy, denoting changes in chromosome number without change in DNA amount through fission/fusion of holocentric chromosomes (chromosomes without localized centromeres). This project includes the creation of bacterial artificial chromosome (BAC) and expressed sequence tagged (EST) libraries to be used in physical and genetic linkage mapping studies in order to reveal the patterns of genome structural variation associated with agmatoploidy in Carex, and to explore the sequence and genic characteristics of chromosomal break points in the genome.