Potato versus grape

Syntenic comparison between grape (y-axis) and potato (x-axis). Potato's genome is assembled into ~68,000 contigs and are ordered from largest to smallest (left to right). Regions with synteny are identifiable based on green dots, but overall the image is difficult to interpret. Results can be regenerated at: http://genomevolution.org/CoGe/SynMap.pl?dsgid1=43;dsgid2=9092;c=4;D=100;g=50;A=5;Dm=;gm=;w=0;b=1;ft1=1;ft2=2;do1=1;do2=1;do=40;dt=geneorder

Specifying the syntenic path assembly option in SynMap

[[image:Master 9092 43.genomic-CDS.blastn.dag.go c4 D100 g50 A5.aligncoords.gcoords ct0.w2000.ass2.png|thumb|600px|right|Syntenic comparison between grape (y-axis) and potato (x-axis) using syntenic path assembly in SynMap. Now contigs are ordered and oriented by their syntenic path through grape. While not perfect, and complicated by a shared [[paleohexaploidy], identifying syntenic regions is much more apparent. Analysis can be regenerated at: http://genomevolution.org/CoGe/SynMap.pl?dsgid1=43;dsgid2=9092;c=4;D=100;g=50;A=5;Dm=;gm=;w=0;b=1;ft1=1;ft2=2;sp=2;do1=1;do2=1;do=40;dt=geneorder]]

In this example, we are comparing the fairly well assembled genome of grape to the contig-level assembly of potato (~68,000 contigs). An initial syntenic dotplot between these genomes using SynMap does reveal some syntenic regions, but finding any specific syntenic region to grape is difficult. By turning on the syntenic path assembly option in SynMap and choosing not to show any chromosomes/contigs without inferred synteny, it becomes much easier to see the large amount of syntenic shared between these genomes.