Difference between revisions of "Angisperm ancestral genome reconstruction"

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(Overview)
(Overview)
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== Overview ==
 
== Overview ==
  
Zheng and Sankoff have developed and continue to refine a mathematical framework for reconstructing ancestral genome states of various angiosperm lineages using [[syntenic blocks]] identified by [[SynMap]], an interactive tool for the pairwise comparison of whole genomes development by Tang and Lyons.  This problem is complicated by [[whole genome duplications]], a common occurrence in angiosperm lineages.   
+
Zheng and Sankoff have developed and continue to refine a mathematical framework for reconstructing ancestral genome states of various angiosperm lineages using [[syntenic blocks]] identified by [[SynMap]], an interactive tool for the pairwise comparison of whole genomes development by Tang and Lyons.  This problem is complicated by [[whole genome duplications]], a common occurrence in angiosperm lineages, followed by [[fractionation]] of duplicated gene content.   
  
Of particular interest are:
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Of particular interest are the ancestral genomes of:
# the ancestral genome of the eudicots which have undergone a [[paleohexaploidy]]
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# Eudicots which have undergone a [[paleohexaploidy]]
 
## [http://www.springerlink.com/content/71656277268rx541/ OMG! Orthologs in Multiple Genomes – Competing Graph-Theoretical Formulations]]
 
## [http://www.springerlink.com/content/71656277268rx541/ OMG! Orthologs in Multiple Genomes – Competing Graph-Theoretical Formulations]]
 
## [http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=6182649&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6182649 Ancient angiosperm hexaploidy meets ancestral eudicot gene order]
 
## [http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=6182649&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6182649 Ancient angiosperm hexaploidy meets ancestral eudicot gene order]
# the ancestral genome of the angiosperms
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# Monocots
## Of current research interest by this team
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# the ancestral genome of the monocots
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## Not possible to solve with the current taxonomic sampling of monocot genomes (currently, only grass genomes are available and of sufficient quality)
 
## Not possible to solve with the current taxonomic sampling of monocot genomes (currently, only grass genomes are available and of sufficient quality)
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## Anticipated high-quality genomes that may help:
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### Banana: http://www.musagenomics.org/
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### Duckweed: http://lemna.rutgers.edu/
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# Angiosperms
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## Of current research interest by this team
 +
 +
== Results ==

Revision as of 19:18, 13 May 2012

Collaboration of:

  • Chunfang Zheng
  • David Sankoff
  • Haibao Tang
  • Eric Lyons

Overview

Zheng and Sankoff have developed and continue to refine a mathematical framework for reconstructing ancestral genome states of various angiosperm lineages using syntenic blocks identified by SynMap, an interactive tool for the pairwise comparison of whole genomes development by Tang and Lyons. This problem is complicated by whole genome duplications, a common occurrence in angiosperm lineages, followed by fractionation of duplicated gene content.

Of particular interest are the ancestral genomes of:

  1. Eudicots which have undergone a paleohexaploidy
    1. OMG! Orthologs in Multiple Genomes – Competing Graph-Theoretical Formulations]
    2. Ancient angiosperm hexaploidy meets ancestral eudicot gene order
  2. Monocots
    1. Not possible to solve with the current taxonomic sampling of monocot genomes (currently, only grass genomes are available and of sufficient quality)
    2. Anticipated high-quality genomes that may help:
      1. Banana: http://www.musagenomics.org/
      2. Duckweed: http://lemna.rutgers.edu/
  3. Angiosperms
    1. Of current research interest by this team

Results