Difference between revisions of "Mimulus v. tomato"

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(→‎Ks histograms of syntenic gene pairs)
(→‎Conclusion: Mean Ks values are smaller for intragenomic comparisons than intergenomic comparisons)
 
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[[File:Screen shot 2012-07-06 at 3.20.46 PM.png|thumb|800px|center| http://genomevolution.org/r/51re]]
 
[[File:Screen shot 2012-07-06 at 3.20.46 PM.png|thumb|800px|center| http://genomevolution.org/r/51re]]
 
[[File:Screen shot 2012-07-06 at 3.21.18 PM.png|thumb|800px|center| http://genomevolution.org/r/51mk]]
 
[[File:Screen shot 2012-07-06 at 3.21.18 PM.png|thumb|800px|center| http://genomevolution.org/r/51mk]]
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== Ks histograms of syntenic gene pairs  ==
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= Ks histograms of syntenic gene pairs  =
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==Conclusion: ==
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Mean Ks values are smaller for intragenomic comparisons than intergenomic comparisons.  Evidence for independent whole genome duplications in the lineages of mimulus and solanum.
  
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===No [[syntenic depth]] screening===
 
{| width="800" border="1" cellpadding="1" cellspacing="1"
 
{| width="800" border="1" cellpadding="1" cellspacing="1"
 
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| Mimulus guttatus  
 
| Mimulus guttatus  
 
| Solanum lycopersicum (tomato)
 
| Solanum lycopersicum (tomato)
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| [[File:Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.min-0.4.log.nsd.hist.png]] http://genomevolution.org/r/51li
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| [[File:Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.min-0.4.log.nsd.hist.png|300px]] http://genomevolution.org/r/51li
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| [[File:Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.min-0.2.max1.log.nsd.hist.png]]http://genomevolution.org/r/51up
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| [[File:Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.min-0.2.max1.log.nsd.hist.png|300px]]]http://genomevolution.org/r/51up
 
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| Mimulus guttatus
 
 
| Solanum lycopersicum (tomato)
 
| Solanum lycopersicum (tomato)
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| [[File:Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.qac1.1.40.gcoords ct0.w800.gene.s.ks.sr.cs1.csoS.min-.4.log.nsd.hist.png]]  http://genomevolution.org/r/51uv
 
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| [[File:Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.qac1.1.40.gcoords ct0.w800.gene.s.ks.sr.cs1.csoS.min-.4.max1.log.nsd.hist.png]] http://genomevolution.org/r/51uw
 
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| Ortholog screening [[1:1 Syntenic depth]]
 
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| Solanum lycopersicum (tomato)
 
| Solanum lycopersicum (tomato)
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| Solanum lycopersicum (tomato)
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| [[File:Master 12289 12289.CDS-CDS.lastz.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w1000.gene.ks.sr.cs1.csoN.log.nsd.hist.png|300px]] http://genomevolution.org/r/51uq
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| [[File:Master 12289 12289.CDS-CDS.lastz.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w1000.gene.ks.sr.cs1.csoN.log.nsd.hist.png]] http://genomevolution.org/r/51uq
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| [[File:Master 12289 12289.CDS-CDS.lastz.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w1000.gene.ks.sr.cs1.csoN.min-.3.max1.log.nsd.hist.png|300px]] http://genomevolution.org/r/4tpr
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| [[File:Master 12289 12289.CDS-CDS.lastz.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w1000.gene.ks.sr.cs1.csoN.min-.3.max1.log.nsd.hist.png]] http://genomevolution.org/r/4tpr
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|  
 
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|-
 
|-
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| Mimulus guttatus
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| Mimulus guttatus
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| [[File:Master 8156 8156.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.log.nsd.hist.png|300px]] http://genomevolution.org/r/51v0
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| [[File:Master 8156 8156.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.min-1.max1.log.nsd.hist.png|300px]]  http://genomevolution.org/r/51v1
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|
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|}
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===1:1 [[syntenic depth]] screening (identified primarily orthologous syntenic gene pairs===
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{| width="800" border="1" cellpadding="1" cellspacing="1"
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|-
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! scope="col" | Org 1
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! scope="col" | Org 2
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! scope="col" | Full Hist
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! scope="col" | Banded Hist
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! scope="col" | Notes
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|-
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| Mimulus guttatus
 
| Solanum lycopersicum (tomato)
 
| Solanum lycopersicum (tomato)
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| [[File:Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.qac1.1.40.gcoords ct0.w800.gene.s.ks.sr.cs1.csoS.min-.4.log.nsd.hist.png|300px]]  http://genomevolution.org/r/51uv
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| [[File:Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.qac1.1.40.gcoords ct0.w800.gene.s.ks.sr.cs1.csoS.min-.4.max1.log.nsd.hist.png|300px]] http://genomevolution.org/r/51uw
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| Ortholog screening 1:1 [[Syntenic depth]]
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|-
 
| Solanum lycopersicum (tomato)
 
| Solanum lycopersicum (tomato)
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|  
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| Solanum lycopersicum (tomato)
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|  
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| [[File:Master 12289 12289.CDS-CDS.lastz.dag.all.go D20 g10 A5.aligncoords.Dm80.ma1.qac1.1.20.gcoords ct0.w1000.gene.ks.sr.cs1.csoN.log.nsd.hist.png|300px]] http://genomevolution.org/r/51v4
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| Ortholog screening [[1:1 Syntenic depth]]
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| [[File:Master 12289 12289.CDS-CDS.lastz.dag.all.go D20 g10 A5.aligncoords.Dm80.ma1.qac1.1.20.gcoords ct0.w1000.gene.ks.sr.cs1.csoN.min-.4.max1.log.nsd.hist.png|300px]]  http://genomevolution.org/r/51v6
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| Ortholog screening 1:1 [[Syntenic depth]]
 
|-
 
|-
 
| Mimulus guttatus
 
| Mimulus guttatus
 
| Mimulus guttatus
 
| Mimulus guttatus
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| [[File:Master 8156 8156.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.log.nsd.hist.png]] http://genomevolution.org/r/51v0
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| [[File:Master 8156 8156.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.qac1.1.40.gcoords ct0.w800.gene.s.ks.sr.cs1.csoS.log.nsd.hist.png|300px ]] http://genomevolution.org/r/51v5
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| [[File:Master 8156 8156.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.min-1.max1.log.nsd.hist.png]]  http://genomevolution.org/r/51v1
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| [[ File:Master 8156 8156.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.qac1.1.40.gcoords ct0.w800.gene.s.ks.sr.cs1.csoS.min-1.max1.log.nsd.hist.png|300px]]  http://genomevolution.org/r/51v3
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|  
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| Ortholog screening 1:1 [[Syntenic depth]]
 
|}
 
|}
  
 
<br>
 
<br>

Latest revision as of 08:03, 7 July 2012

Note: evaluation of tomato is difficult as its polyploidy is not a string tetraploidy or hexaploidy: Tomato genome

Whole genome syntenic dotplots

http://genomevolution.org/r/518r

High-resolution analysis of syntenic regions with GEvo

Fractionation appears to be independent among intragenomic syntenic regions

http://genomevolution.org/r/51re
http://genomevolution.org/r/51mk

Ks histograms of syntenic gene pairs

Conclusion:

Mean Ks values are smaller for intragenomic comparisons than intergenomic comparisons. Evidence for independent whole genome duplications in the lineages of mimulus and solanum.

No syntenic depth screening

Org 1 Org 2 Full Hist Banded Hist Notes
Mimulus guttatus Solanum lycopersicum (tomato) Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.min-0.4.log.nsd.hist.png http://genomevolution.org/r/51li Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.min-0.2.max1.log.nsd.hist.png]http://genomevolution.org/r/51up
Solanum lycopersicum (tomato) Solanum lycopersicum (tomato) Master 12289 12289.CDS-CDS.lastz.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w1000.gene.ks.sr.cs1.csoN.log.nsd.hist.png http://genomevolution.org/r/51uq Master 12289 12289.CDS-CDS.lastz.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w1000.gene.ks.sr.cs1.csoN.min-.3.max1.log.nsd.hist.png http://genomevolution.org/r/4tpr
Mimulus guttatus Mimulus guttatus Master 8156 8156.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.log.nsd.hist.png http://genomevolution.org/r/51v0 Master 8156 8156.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w800.ass.gene.s.ks.sr.cs1.csoS.min-1.max1.log.nsd.hist.png http://genomevolution.org/r/51v1

1:1 syntenic depth screening (identified primarily orthologous syntenic gene pairs

Org 1 Org 2 Full Hist Banded Hist Notes
Mimulus guttatus Solanum lycopersicum (tomato) Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.qac1.1.40.gcoords ct0.w800.gene.s.ks.sr.cs1.csoS.min-.4.log.nsd.hist.png http://genomevolution.org/r/51uv Master 8156 12289.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.qac1.1.40.gcoords ct0.w800.gene.s.ks.sr.cs1.csoS.min-.4.max1.log.nsd.hist.png http://genomevolution.org/r/51uw Ortholog screening 1:1 Syntenic depth
Solanum lycopersicum (tomato) Solanum lycopersicum (tomato) Master 12289 12289.CDS-CDS.lastz.dag.all.go D20 g10 A5.aligncoords.Dm80.ma1.qac1.1.20.gcoords ct0.w1000.gene.ks.sr.cs1.csoN.log.nsd.hist.png http://genomevolution.org/r/51v4 Master 12289 12289.CDS-CDS.lastz.dag.all.go D20 g10 A5.aligncoords.Dm80.ma1.qac1.1.20.gcoords ct0.w1000.gene.ks.sr.cs1.csoN.min-.4.max1.log.nsd.hist.png http://genomevolution.org/r/51v6 Ortholog screening 1:1 Syntenic depth
Mimulus guttatus Mimulus guttatus Master 8156 8156.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.qac1.1.40.gcoords ct0.w800.gene.s.ks.sr.cs1.csoS.log.nsd.hist.png http://genomevolution.org/r/51v5 Master 8156 8156.CDS-CDS.last.dag.all.go D20 g10 A5.aligncoords.qac1.1.40.gcoords ct0.w800.gene.s.ks.sr.cs1.csoS.min-1.max1.log.nsd.hist.png http://genomevolution.org/r/51v3 Ortholog screening 1:1 Syntenic depth


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