Difference between revisions of "Ancestral angiosperm genomes"
From CoGepedia
(Created page with 'Phylogeny of the Angiosperms with polyploidy events marked. Branch lengths are meaningless.') |
(→Pre-hexaploid eudicot ancestor) |
||
| (5 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | [[File:Screen shot 2012-06-18 at 10.51.11 AM.png|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 and David Sankoff | ||
| + | # 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 Cacao]] | ||
| + | |||
| + | [[Eurosid Ancestor to Peach]] | ||
| + | |||
| + | [[Eurosid Ancestor to Amborella]] | ||
| + | |||
| + | ==Pre-hexaploid eudicot ancestor== | ||
| + | # Data generated by Chungfang Zheng and David Sankoff | ||
| + | # 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 | ||
| + | |||
| + | |||
| + | [[Paleohex Ancestor to Paleohex Ancestor]] | ||
| + | |||
| + | [[Paleohex Ancestor to Grape]] | ||
| + | |||
| + | [[Paleohex Ancestor to Cacao]] | ||
| + | |||
| + | [[Paleohex Ancestor to Peach]] | ||
| + | |||
| + | [[Paleohex Ancestor to Nelumbo]] | ||
| + | |||
| + | [[Paleohex Ancestor to Amborella]] | ||
Latest revision as of 11:43, 19 June 2012
Ancestral Eurosid
- Data generated by Chungfang Zheng and David Sankoff
- 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
Pre-hexaploid eudicot ancestor
- Data generated by Chungfang Zheng and David Sankoff
- 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
