Tomato-Utricularia Syntenic Depth

Follow this link for information on Syntenic depth.

Syntenic depth measurements permit classifying the number of whole genome duplications that have happened in one lineage relative to another. Unfortunately, these analyses are not 100% conclusive, but provide supporting evidence, especially when combined with Syntenic dotplots.

Using v4 of the Utricularia genome (http://genomevolution.org/CoGe//OrganismView.pl?dsgid=19456)

4 genes in an 80 gene window

SynFind: http://genomevolution.org/r/4tqx

Utricularia gibba

Depth 1	6972	of	19459	35.83%
Depth 2	4727	of	19459	24.29%
Depth 3	3392	of	19459	17.43%
Depth 4	2153	of	19459	11.06%
Depth 5	1230	of	19459	6.32%
Depth 6	603	of	19459	3.10%
Depth 7	223	of	19459	1.15%
Depth 8	118	of	19459	0.61%
Depth 9	39	of	19459	0.20%
Depth 10	2	of	19459	0.01%

4 genes in a 40 gene window

SynFind: http://genomevolution.org/r/4tqi

Utricularia gibba

Depth 1	5566	of	8468	65.73%
Depth 2	2071	of	8468	24.46%
Depth 3	664	of	8468	7.84%
Depth 4	137	of	8468	1.62%
Depth 5	25	of	8468	0.30%
Depth 6	5	of	8468	0.06%

Materials and Methods

Syntenic Depth tables are calculated by CoGe's tool SynFind. These analyses used Last Kiełbasa, S. M., Wan, R., Sato, K., Horton, P., and Frith, M. C. (2011). "Adaptive Seeds Tame Genomic Sequence Comparison". Genome Res 21: 487-493.  to compare protein coding sequences of these genomes and Synteny_Score to identify syntenic regions. Synteny_Score is part of the TangTools {{cite web |author=Haibao Tang |title=TangTools | url=https://github.com/tanghaibao/quota-alignment }