Syntenic depth

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Syntenic depth refers to the number of times a genomic region (or genome) is syntenic to regions in another genome.

Tools in CoGe for classifying and quantitating syntenic depth:

Examples:

Organism Syntenic Depth
Dotpot
E. coli DH10B to MG1655
1:1
Screen shot 2012-03-27 at 2.50.26 PM.png
Human-Chimp 1:1 Screen shot 2012-03-27 at 2.59.25 PM.png
Rice-Brachypodium
2:2
Screen shot 2012-03-27 at 2.53.56 PM.png
Sorghum-Maize 2:4 Screen shot 2012-03-27 at 3.00.43 PM.png

Syntenic Depth Tables

SynFind Syntenic Depth Examples

These tables show the number of gene participating at a particular syntenic depth and are used to infer the number of polyploidy events between two genomes.

Syntenic Dopltot Syntenic Depth Calculation Known History
Screen shot 2012-03-27 at 2.53.56 PM.png Screen shot 2012-03-28 at 8.48.43 AM.png

Obvious 2:2 depth.

Share a recent whole genome duplication. Also share older whole genome duplictions (at least one)