Homologous gene detection in diverse plant proteomes. (A) Blastx: The complete unigene set was queried against the complete set of predicted proteins in the genomes of Arabidopsis thaliana, Physcomitrella patens, and Selaginella moellendorfii using an e-value cut off of 1e-5. Unigenes with positive hits in more than one proteome are shown in the intersect for those species. Of 56,256 total unigenes, 21,425 unigenes did not have a positive blast hit. (B) PlantTribes OrthoGroups: Unigenes were assigned to Tribe- and OrthoMCL clusters derived from the updated PlantTribes classification based on the best blast hit for each unigene. The presence of genes from Arabidopsis thaliana, Physcomitrella patens, and Selaginella moellendorfii in each OrthoGroup was evaluated. Of 56,256 total unigenes, 18,368 unigenes were not assigned to an OrthoGroup cluster and an additional 2,309 were assigned to clusters having no homologs from Arabidopsis, Physcomitrella, or Selaginella.