Ancestral angiosperm genomes: Difference between revisions
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[[File:Screen shot 2012-06-18 at 10.51.11 AM.png|thumb|center|800px|Phylogeny of the Angiosperms with polyploidy events marked. Branch lengths are meaningless.]] | [[File:Screen shot 2012-06-18 at 10.51.11 AM.png|thumb|center|800px|Phylogeny of the Angiosperms with polyploidy events marked. Branch lengths are meaningless.]] | ||
==Ancestral Eurosid== | |||
# Data generated by Chungfang Zheng | |||
# Procedure for generating ancestral genome: | |||
## Take ancestral ortholog sets from grape/chocolate/peach | |||
## Use the ortholog gene from first grape, then chocolate, then peach (if data is missing) | |||
## Extract CDS sequence from CoGe | |||
## Reverse complement if necessary | |||
## Print sequence | |||
## Pad with 1000 "N"s between coding sequence | |||
Link to ancestral genome: http://genomevolution.org/CoGe/OrganismView.pl?oid=38348 | |||
===Syntenic dotplots=== | |||
[[Eurosid Ancestor to Eurosid Ancestor]] | |||
[[Eurosid Ancestor to Grape]] | |||
[[Eurosid Ancestor to Amborella]] | |||
Revision as of 18:18, 18 June 2012
Ancestral Eurosid
- Data generated by Chungfang Zheng
- Procedure for generating ancestral genome:
- Take ancestral ortholog sets from grape/chocolate/peach
- Use the ortholog gene from first grape, then chocolate, then peach (if data is missing)
- Extract CDS sequence from CoGe
- Reverse complement if necessary
- Print sequence
- Pad with 1000 "N"s between coding sequence
Link to ancestral genome: http://genomevolution.org/CoGe/OrganismView.pl?oid=38348