Putative single-copy genes and conserved ortho-log sets (COS) were identified in model plant species thale cress (Arabidopsis thaliana), rice (Oryza sativa ssp. japonica), and poplar [black cottonwood, Populus tricho-carpa (Torr. & Gray ex Brayshaw)] and used to find putative COS in four conifers (the Coniferales order). Using expressed sequence tag sequences, unique transcript sets were assembled in loblolly pine (Pinus taeda L.), white spruce [Picea glauca (Moench) Voss], Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii], and sugi [Cryptomeria japonica (Thunberg ex Linnaeus f.) D. Don]. They were compared with COS sets identified in three model plant species using comparative sequence analysis. Almost half of the single-copy genes in herba-ceous species (Arabidopsis and rice) had additional copies and homologs in poplar and conifers. The identified tentative COS sets have many applications in evolutionary genomics studies, phylogenetic analysis, and comparative mapping.