Mimulus v. tomato: Difference between revisions

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Note: evaluation of tomato is difficult as its polyploidy is not a string tetraploidy or hexaploidy:  [[Tomato genome]]
==Whole genome [[syntenic dotplots]]==
[[File:Screen shot 2012-07-06 at 12.32.07 PM.png|thumb|800px|center|http://genomevolution.org/r/518r]]
[[File:Screen shot 2012-07-06 at 12.32.07 PM.png|thumb|800px|center|http://genomevolution.org/r/518r]]
==High-resolution analysis of syntenic regions with [[GEvo]]==
Fractionation appears to be independent among intragenomic syntenic regions
[[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]]
= 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===
{| width="800" border="1" cellpadding="1" cellspacing="1"
|-
! scope="col" | Org 1
! scope="col" | Org 2
! scope="col" | Full Hist
! scope="col" | Banded Hist
! scope="col" | Notes
|-
| Mimulus guttatus
| Solanum lycopersicum (tomato)
| [[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
| [[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
|
|-
| Solanum lycopersicum (tomato)
| Solanum lycopersicum (tomato)
| [[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
| [[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
|
|-
| Mimulus guttatus
| Mimulus guttatus
| [[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
| [[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
|
|}
===1:1 [[syntenic depth]] screening (identified primarily orthologous syntenic gene pairs===
{| width="800" border="1" cellpadding="1" cellspacing="1"
|-
! scope="col" | Org 1
! scope="col" | Org 2
! scope="col" | Full Hist
! scope="col" | Banded Hist
! scope="col" | Notes
|-
| Mimulus guttatus
| Solanum lycopersicum (tomato)
| [[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
| [[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
| Ortholog screening 1:1 [[Syntenic depth]]
|-
| Solanum lycopersicum (tomato)
| Solanum lycopersicum (tomato)
| [[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
| [[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
| Ortholog screening 1:1 [[Syntenic depth]]
|-
| Mimulus guttatus
| Mimulus guttatus
| [[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
| [[ 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
| Ortholog screening 1:1 [[Syntenic depth]]
|}
<br>

Latest revision as of 15:03, 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) http://genomevolution.org/r/51li ]http://genomevolution.org/r/51up
Solanum lycopersicum (tomato) Solanum lycopersicum (tomato) http://genomevolution.org/r/51uq http://genomevolution.org/r/4tpr
Mimulus guttatus Mimulus guttatus http://genomevolution.org/r/51v0 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) http://genomevolution.org/r/51uv http://genomevolution.org/r/51uw Ortholog screening 1:1 Syntenic depth
Solanum lycopersicum (tomato) Solanum lycopersicum (tomato) http://genomevolution.org/r/51v4 http://genomevolution.org/r/51v6 Ortholog screening 1:1 Syntenic depth
Mimulus guttatus Mimulus guttatus http://genomevolution.org/r/51v5 http://genomevolution.org/r/51v3 Ortholog screening 1:1 Syntenic depth


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