Lack of Synteny Between Selaginella and Physcomitrella patens, Oryza sativa japonica, and Vitis vinifera
From Purdue Genomics Database Facility
Syntenic dotplots were created for the following pairs of organisms:
- Selaginella moellendorfii versus Physcomitrella patens
- Selaginella moellendorfii versus Oryza sativa japonica
- Selaginella moellendorfii versus Vitis vinifera
These organisms were chosen for their placement in land plant phylogeny, and their relative genomic simplicity with regards to whole genome duplication events. Physcomitrella patens is an early branching land plant that is basal to vascular plants and Selaginella. Oryza sativa japonica is one of several grass genomes currently sequenced, and while containing at least two whole genome duplication events, there are no other more basal monocot genomes yet available. Vitis vinifera is a basal (or sister to) eudicot, derived from a hexaploid genome whose origin predated the divergence of the eurosid and asterid lineages.
The following syntenic dotplots were generated using SynMap (http://synteny.cnr.berkeley.edu/SynMap.pl). This tools uses blastn to comparing all coding regions in order to identify putative homologous gene pairs and DAGChainer to infer synteny by identifying collinear sets of putative homologous gene pairs. In all cases, there are no identified syntenic regions between Selaginella and these organisms. For example of syntenic dotplot images with the signature of synteny, please see Whole Genome Syntenic Analysis of Haplotypes
Selaginella moellendorfii versus Physcomitrella patens
Selaginella moellendorfii versus Oryza sativa japonica
Selaginella moellendorfii versus Vitis vinifera
References
To be generated upon request.
