The chromosomal organization of genes, or chromosomal map, is specific to each species. The comparison of chromosomal maps has however shown that closely related organisms show large segments in which the gene content and organization are conserved. The local conservations, called conserved syntenies or simply syntenies, as well as the associated ruptures are the consequences of the evolutionary remodelling of the chromosomes.

The advent of complete genome sequences offers the possibility to study in greater details the extent of genome conservation. The recent comparison of the complete genomes of human and mouse for example showed that in addition to the large conserved syntenic regions, other regions seem to be mosaics of very small conserved segments. Moreover, globally conserved regions show frequently small local rearrangements.

In order to study the genome conservation and organisation in plants, a strategy for constructing a hierarchy of conservations starting with elementary segments of strongly conserved sequences (>100bp) and ending with conserved syntenies covering several megabases is embedded in a tool, called Narcisse, which enables in addition to navigate in these various levels of conservation.