Tomato genome

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Tomato genome published in Nature

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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.

High-resolution syntenic analysis of tomato v. grapevine