Ancestral angiosperm genomes

Phylogeny of the Angiosperms with polyploidy events marked. Branch lengths are meaningless.

Ancestral Eurosid

1. Data generated by Chungfang Zheng and David Sankoff
2. Procedure for generating ancestral genome:
   1. Take ancestral ortholog sets from grape/chocolate/peach
   2. Use the ortholog gene from first grape, then chocolate, then peach (if data is missing)
   3. Extract CDS sequence from CoGe
   4. Reverse complement if necessary
   5. Print sequence
   6. 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

1. Data generated by Chungfang Zheng and David Sankoff
2. Procedure for generating ancestral genome:
   1. Take ancestral ortholog sets from grape/chocolate/peach
   2. Use the ortholog gene from first grape, then chocolate, then peach (if data is missing)
   3. Extract CDS sequence from CoGe
   4. Reverse complement if necessary
   5. Print sequence
   6. 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