Syntenic dotplot

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Syntenic dotplot of E-coli B strain REL606(x-axis) and E-coli K12 strain DH10B (y-axis). The "green" line represents the regions of similarities between the two genomes while the discontinuities in this syntenic line (marked by numbered arrows) represent regions of genomic variations at a given locus between the two substrains of E-coli. Variations of this size (10s of kb) are usually the result of phage insertions, horizontal gene transfer events, deletions, and transposon activity. More information about this comparison can be found here. More examples of bacterial syntenic dotplots and x-alignments can be found here. This dotplot can be regenerated here.
Syntenic dotplot with Ks coloration of sorghum (x-axis) versus maize (y-axis). Genes are used for axis metrics; black lines separate chromosomes in each genome. Results can be regenerated at: Red syntenic lines are from the maize-specific whole genome duplication event and are orthologous to sorghum. Purple are from the older pre-grass whole genome duplication event are are out-paralogs. More information about this analysis can be found here.
Syntenic dotplot of poplar versus itself. Syntenic gene-pairs are colored by the synonymous mutation values. This reveals intragenomic synteny derived from a recent whole genome duplication event (dark blue) and the older eudicot paleohexaploidy event (green-cyan). This analysis can be regenerated at;dsgid2=8154;c=4;D=40;g=20;A=5;Dm=;gm=;w=0;b=1;ft1=1;ft2=1;do1=1;do2=1;do=40;dt=geneorder;ks=1;am=g
Histogram of the synonymous mutation (Ks) values (log 10 transformed) of the syntenic gene pairs within poplar. Smaller values on left infers young gene pairs, and larger values on right infers older gene pairs. The two middle peaks are from poplar's recent whole genome duplication event (blue) and a more ancient eudicot paleohexaploidy event (green-cyan). The peak on the far right, with non-log10 transformed Ks values of 50-100 are noise in the analysis. Perhaps from the alignment of pseudogenes, mis-called syntenic gene pairs, and erroneous gene models. These colors correspond to the colors used in the syntenic dotplot shown above.

Syntenic dotplots are a type of scatter-plot. Each axis represents a sequence laid end-to-end, and each dot in the scatter-plot represents a putative homologous match between the two sequences. Often, these dotplots are used for whole genome comparisons within the same genome or across two genomes from different taxa in order to identify synteny. Synteny is defined as two or more genomic regions that are derived from a common ancestral genomic region. The evidence for synteny is the identification of a set of homologous genes in two genome that have a collinear arrangement. When such a pattern of gene-order conservation is discovered, the most parsimonious explanation is that the two regions are related through a common ancestor. While syntenic dotplots are useful for identifying related genomic regions, they are also useful for identifying genomic regions that have undergone an evolutionary change in one of the two genomes being compared. Example of such events are:

CoGe's tool SynMap makes it easy to create a syntenic dotplot for any two genomes in CoGe.