Related Experiment Video
Updated: Jun 23, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
Published on: December 22, 2017
Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus
Xiaohan Yang1, Sara Jawdy, Timothy J Tschaplinski
1Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA.
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 OryzaSS 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.
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Cell Signaling in Plants

