Abstract
Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential
gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant
transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine,
Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression,
protein motif and intron number were examined. 192, 641 and 109 SS genes were identified in
Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers,
roots, xylem and cambium or up-regulated by stress. Six conserved motifs in Arabidopsis and Oryza SS
proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes.
The results reflect functional and/or anatomical differences between monocots and eudicots or between
herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and
biofuel research.
