Nelumbo v. Amborella: Difference between revisions
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[[File:Screen shot 2012-04-10 at 12.03.32 PM.png|thumb|center|600px|[[Syntenic dotplot]] of Ambroella (x-axis) to Nelumbo (y-axis). Note that each region of Amborella is syntenic to two regions of Nelumbo. Results may be regenerated at: http://genomevolution.org/r/4pcd]] | [[File:Screen shot 2012-04-10 at 12.03.32 PM.png|thumb|center|600px|[[Syntenic dotplot]] of Ambroella (x-axis) to Nelumbo (y-axis). Note that each region of Amborella is syntenic to two regions of Nelumbo. Results may be regenerated at: http://genomevolution.org/r/4pcd]] | ||
Interestingly, SynFind's syntenic depth calculation shows: | |||
<pre> | |||
Syntenic Depth: | |||
Nelumbo nucifera (sacred lotus) | |||
Depth 1 5222 of 18684 27.95% | |||
Depth 2 11809 of 18684 63.20% | |||
Depth 3 1217 of 18684 6.51% | |||
Depth 4 406 of 18684 2.17% | |||
Depth 5 24 of 18684 0.13% | |||
Depth 6 6 of 18684 0.03% | |||
</pre> | |||
Shows that there may be a 1:4 amborella to Nelumbo. This would mean that Nelumbo is a double tetraploidy. Results may be regenerated at: http://genomevolution.org/r/4pd9 | |||
==GEvo Analyses of 1:4 [[syntenic depth]] regions== | |||
[[File:Screen shot 2012-04-10 at 3.12.01 PM.png|thumb|center|600px|[[GEvo]] analysis of a 1xAmborella : 4xNelumbo syntenic regions. Note that the Amborella regions is divided between the two pairs of Nelumbo regions. Results may be regenerated at: http://genomevolution.org/r/4pdi]] | |||
[[File:Screen shot 2012-04-10 at 4.06.31 PM.png |thumb|center|600px|[[GEvo]] analysis of a 1xAmborella : 4xNelumbo syntenic regions. Note that the Amborella regions is divided between the two pairs of Nelumbo regions. Results may be regenerated at: http://genomevolution.org/r/4ped]] | |||
[[File:Screen shot 2012-04-10 at 4.15.16 PM.png|thumb|center|600px|[[GEvo]] analysis of a 1xAmborella : 4xNelumbo syntenic regions. Note that the Amborella regions is divided between the two pairs of Nelumbo regions. Results may be regenerated at: http://genomevolution.org/r/4pef]] | |||
[[File:Screen shot 2012-04-10 at 3.26.43 PM.png|thumb|center|600px|[[GEvo]] analysis of a 1xAmborella : 4xNelumbo syntenic regions. All four Nelumbo regions show [[intercalated synteny]] to Ambroella. Results may be regenerated at http://genomevolution.org/r/4pdt]] | |||
[[File:Screen shot 2012-04-10 at 4.01.01 PM.png|thumb|center|600px|[[GEvo]] analysis of a 1xAmborella : 4xNelumbo syntenic regions. All four Nelumbo regions show [[intercalated synteny]] to Ambroella. Results may be regenerated at http://genomevolution.org/r/4pea]] | |||
[[File:Screen shot 2012-04-10 at 4.09.20 PM.png|thumb|center|600px|[[GEvo]] analysis of a 1xAmborella : 4xNelumbo syntenic regions. All four Nelumbo regions show [[intercalated synteny]] to Ambroella. Results may be regenerated at http://genomevolution.org/r/4pee]] | |||
Latest revision as of 23:16, 10 April 2012
Interestingly, SynFind's syntenic depth calculation shows:
Syntenic Depth: Nelumbo nucifera (sacred lotus) Depth 1 5222 of 18684 27.95% Depth 2 11809 of 18684 63.20% Depth 3 1217 of 18684 6.51% Depth 4 406 of 18684 2.17% Depth 5 24 of 18684 0.13% Depth 6 6 of 18684 0.03%
Shows that there may be a 1:4 amborella to Nelumbo. This would mean that Nelumbo is a double tetraploidy. Results may be regenerated at: http://genomevolution.org/r/4pd9
GEvo Analyses of 1:4 syntenic depth regions
