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The image above shows a syntenic alignment between genomic regions of grape and tomato. Nearly every gene in grape has a syntenic match to tomato (the tomato genomic region is not annotated). This near-perfect one-to-one mapping of gene between fairly distantly related plant genomes (one from each of two major groups of eudicots -- eurosids and astrids) is the expected pattern if neither genome has undergone one or more independent whole genome duplication (WGD) events. In plants, following WGD, each duplicated genomic region undergoes diploidization, which reduces the total gene content of the genome to one which is more similar to the pre-duplicated ancestor genome. This process of gene loss is known as fractionation and results in distributing ancestral gene content over all genomic duplicates. If such a process were at work, we would not expect to see the near-perfect one-to-one mapping of gene content. Results can be regenerated and analysis resumed using http://tinyurl.com/qjpcvv.
==SynMap comparison of Arabidopsis thaliana and Arabidopsis lyrata showing how syntenic regions derived from different whole genome duplications are comprised of syntelogs with characteristic different synonymous mutation rates
This syntenic dotplot is between two Arabidopsis species, A. lyrata on the x-axis and A. thaliana on the y-axis. Each putative homologous match between two genes results in a gray dot being drawn on the plot. The results are analyzed by DAGChainer to identify syntenic regions and syntelogous gene pairs are analyzed by CODEML to calculate their synonymous mutation rate. This dotplot shows extensive stretches of synteny between these two genomes in a two-to-two relationship. Each genomic region is syntenic to two region in the other genome. One that is orthologous and derived from the speciation of the lineages, and the other from a shared whole genome duplication event.