Difference between revisions of "Tomato genome"
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[[File:Screen Shot 2012-06-01 at 7.40.54 AM.png]] | [[File:Screen Shot 2012-06-01 at 7.40.54 AM.png]] | ||
| − | + | * 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)= | =Solanum-specific paleohexaploidy (whole genome triplication)= | ||
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"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." | "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: | + | =Further comparisons using CoGe: evidence for a solanum specific hexaploidy or tetraploidy event= |
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| + | These analyses do not provide a clear-cut explanation of the evolutionary history of tomato. Please join a discussion and share your throughts on these results on CoGe's Forums (hosted by iPlant): https://forums.iplantcollaborative.org/viewtopic.php?f=10&t=92 | ||
| + | |||
| + | ==Tomato versus tomato (itself)== | ||
| + | If tomato has a lineage specific hexaploidy, comparison to iself should show a strong 3:3 syntenic signal in the [[syntenic dotplot]] if its genome to itself. This should be readily apparent [[Ks]] value calculations. However, the [[syntenic dotplot]] of tomato versus itself shows a strong 2:2 [[syntenic depth]] (one additional syntenic region to each region of its genome). | ||
| + | * [[Tomato v. tomato]] | ||
==Tomato versus potato== | ==Tomato versus potato== | ||
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==Tomato versus grape== | ==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. | + | 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. |
* [[Tomato v. grapevine]] | * [[Tomato v. grapevine]] | ||
| + | |||
| + | ==High-resolution analysis using [[GEvo]] for comparing a tomato triplicate region with grape as an outgroup== | ||
| + | |||
| + | If a region in tomato was triplicated, it should show the classic pattern of [[fractionation]] among [[homeologous]] genes when compared to an outgroup region from a genome without the polyploidy event. This is the exact pattern observed using grape as an outgroup. | ||
| + | |||
| + | [[High-resolution syntenic analysis of tomato v. grapevine]] | ||
Latest revision as of 10:13, 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: evidence for a solanum specific hexaploidy or tetraploidy event
These analyses do not provide a clear-cut explanation of the evolutionary history of tomato. Please join a discussion and share your throughts on these results on CoGe's Forums (hosted by iPlant): https://forums.iplantcollaborative.org/viewtopic.php?f=10&t=92
Tomato versus tomato (itself)
If tomato has a lineage specific hexaploidy, comparison to iself should show a strong 3:3 syntenic signal in the syntenic dotplot if its genome to itself. This should be readily apparent Ks value calculations. However, the syntenic dotplot of tomato versus itself shows a strong 2:2 syntenic depth (one additional syntenic region to each region of its genome).
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.
High-resolution analysis using GEvo for comparing a tomato triplicate region with grape as an outgroup
If a region in tomato was triplicated, it should show the classic pattern of fractionation among homeologous genes when compared to an outgroup region from a genome without the polyploidy event. This is the exact pattern observed using grape as an outgroup.
