Difference between revisions of "Tomato genome"
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=Further comparisons using CoGe: Lack of evidence for a solanum specific hexaploidy= | =Further comparisons using CoGe: Lack of evidence for a solanum specific hexaploidy= | ||
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| + | ==Tomato versus potato== | ||
If tomato and potato share a common recent hexaploidy, there should be a strong 1:3 syntenic signal in the [[syntenic dotplot]] of these genomes. With [[Ks]] value calculations, we would expect to see a strong orthologous region and two [[out-paralogous]] regions of approximately equal ages. However, analysis of these genomes in SynMap reveals one strong orthologous region and one [[out-paralogous]] region, which supports a shared tetraploidy. Interestingly, there are a couple of regions that show two [[out-paralogous]] regions. | If tomato and potato share a common recent hexaploidy, there should be a strong 1:3 syntenic signal in the [[syntenic dotplot]] of these genomes. With [[Ks]] value calculations, we would expect to see a strong orthologous region and two [[out-paralogous]] regions of approximately equal ages. However, analysis of these genomes in SynMap reveals one strong orthologous region and one [[out-paralogous]] region, which supports a shared tetraploidy. Interestingly, there are a couple of regions that show two [[out-paralogous]] regions. | ||
| − | [[Tomato v. potato]] | + | # [[Tomato v. potato]] |
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| + | ==Tomato versus grape== | ||
| + | If tomato has a lineage specific hexaploidy, comparison to the grape genome (which only has the eudicot [[paleohexaploidy]])) should show a 1:3 [[syntenic depth]] of orthologous regions, and a might weaker signal for their shared eudicot [[paleohexaploidy]]. However, analysis of the syntenic dotplot of these genomes (with Ks coloration), shows a strong 1:2 syntenic mapping of orthologous regions. | ||
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| + | # [[Tomato v. grapevine]] | ||
Revision as of 09:10, 1 June 2012
Contents
Tomato genome published in Nature
- Issue: http://www.nature.com/nature/journal/v485/n7400/
- Nature Commentary: http://www.nature.com/nature/journal/v485/n7400/full/485547a.html
- Nature Article: http://www.nature.com/nature/journal/v485/n7400/full/nature11119.html
- The tomato genome sequence provides insights into fleshy fruit evolution
Solanum-specific paleohexaploidy (whole genome triplication)
From: tomato genome sequence provides insights into fleshy fruit evolution
"Comparison with the grape genome also reveals a more recent triplication in tomato and potato. Whereas few individual tomato/potato genes remain triplicated (Supplementary Tables 10 and 11), 73% of tomato gene models are in blocks that are orthologous to one grape region, collectively covering 84% of the grape gene space. Among these grape genomic regions, 22.5% have one orthologous region in tomato, 39.9% have two, and 21.6% have three, indicating that a whole-genome triplication occurred in the Solanum lineage, followed by widespread gene loss. This triplication, also evident in potato (Supplementary Fig. 11), is estimated at 71 (±19.4) Myr on the basis of the Ks of paralogous genes (Supplementary Fig. 10), and therefore predates the ~7.3 Myr tomato–potato divergence."
Further comparisons using CoGe: Lack of evidence for a solanum specific hexaploidy
Tomato versus potato
If tomato and potato share a common recent hexaploidy, there should be a strong 1:3 syntenic signal in the syntenic dotplot of these genomes. With Ks value calculations, we would expect to see a strong orthologous region and two out-paralogous regions of approximately equal ages. However, analysis of these genomes in SynMap reveals one strong orthologous region and one out-paralogous region, which supports a shared tetraploidy. Interestingly, there are a couple of regions that show two out-paralogous regions.
Tomato versus grape
If tomato has a lineage specific hexaploidy, comparison to the grape genome (which only has the eudicot paleohexaploidy)) should show a 1:3 syntenic depth of orthologous regions, and a might weaker signal for their shared eudicot paleohexaploidy. However, analysis of the syntenic dotplot of these genomes (with Ks coloration), shows a strong 1:2 syntenic mapping of orthologous regions.
