Pre-genomic discovery of parallel arrangement in morphological and isozyme markers among different taxa rationalized the continuation of such studies at the DNA level, revealing significant co-linearity across even divergent plant taxa (Bowers et al. 2005; Salse et al. 2008; Tang et al. 2008a). Large-scale genome sequencing efforts coupled with strong computational algorithms have provided a detailed view of the complex evolutionary forces that shaped the structure of eukaryotic chromosomes (Eichler and Sankoff 2003) which are discussed in the following sections.
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