A Phylostratigraphic Approach to Determine Gene Ancestry in the Bryophytes

Comparative genomic analyses are no longer restricted to the comparison of a small number of rather closely related angiosperm species or very distantly related species. Publicly available genomes start to cover evolutionary distances ranging from close and intermediate to distant relationships. Due to this dense species relation grid, evolutionary footprints can now be intensely investigated. Here, to determine the phylogenetic origin of genes in bryophytes a phylostratigraphy approach introduced by Domazet-Loso et al. (2007) is used. To construct such a phylostratigraphic map for bryophytes, the version 3 Physcomitrella patens genome sequence and the longest predicted ORFs of transcript data from a subset of species from the 1KP project (http://www.onekp.com/) are used. On first instance an existing chrono tree serves as a positioning template to assign each available bryophyte protein to a distinct phylostratum (“gene age”). In a second step the evaluated sequences may be used to reconstruct the phylogenetic relations and incorporate more species from the 1KP project. In general this phylostratigraphic approach will help to determine gene ancestry among bryophytes. For P. patens and the upcoming version 3 genome the constructed phylostratigraphic map can then be used to draw conclusions for gene conservation and synteny.