Angisperm ancestral genome reconstruction: Difference between revisions
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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: | Of particular interest are the ancestral genomes of: | ||
# | # 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 | # Monocots | ||
## Not possible to solve with the current taxonomic sampling of monocot genomes (currently, only grass genomes are available and of sufficient quality) | |||
## Anticipated high-quality genomes that may help: | |||
### Banana: http://www.musagenomics.org/ | |||
### Duckweed: http://lemna.rutgers.edu/ | |||
# Angiosperms | |||
## Of current research interest by this team | ## Of current research interest by this team | ||
== Results == | |||
Revision as of 01:18, 14 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:
- Eudicots which have undergone a paleohexaploidy
- Monocots
- Not possible to solve with the current taxonomic sampling of monocot genomes (currently, only grass genomes are available and of sufficient quality)
- Anticipated high-quality genomes that may help:
- Banana: http://www.musagenomics.org/
- Duckweed: http://lemna.rutgers.edu/
- Angiosperms
- Of current research interest by this team