Intercalated Synteny is observed by comparing a genome that has undergone a whole genome duplication followed by fractionation to an outgroup syntenic region that has not undergone fractionation. Members of syntenic gene pairs in the outgroup region are intercalated with regards to the fractionated genomic regions.
Example GEvo analysis of fraction of gene content between 4 syntenic regions of Arabidopsis thaliana and one syntenic region of Carica papaya. Papaya is in the middle with 2 Arabidopsis regions above and below. Since their divergence, Arabidopsis thaliana has had two whole genome duplication events while papaya has had none. After each whole genome duplication event in Arabidopsis, duplicated genes are lost from one homeologous region or the other. Thus, this single region of papaya contains nearly the entire gene content of the four syntenic Arabidopsis regions. Note that some families of genes are retained preferentially following a whole genome duplication event, and that some genes transpose. This analysis can be regenerated at: http://tinyurl.com/o6xnea