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. 165, 638 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.
| Original language | English |
|---|---|
| Pages (from-to) | 473-480 |
| Number of pages | 8 |
| Journal | Genomics |
| Volume | 93 |
| Issue number | 5 |
| DOIs | |
| State | Published - May 2009 |
Funding
We thank Stan Wullschleger and Udaya Kalluri for reviewing the manuscript and valuable comments, and J.C. Tuskan for input on the design of the study. Funding for this research was provided by the U.S. Department of Energy, Office of Science, Biological and Environmental Research Carbon Sequestration Program. ORNL is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.
Keywords
- Arabidopsis
- Gene expression
- Lineage-specific genes
- Perennial plants
- Poplar
- Rice
- Woody plants