Genome-wide Identification of Lineage Specific Genes in Arabidopsis, Oryza and Populus

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1 Genome-wide Identification of Lineage Specific Genes in Arabidopsis, Oryza and Populus Xiaohan Yang Sara Jawdy Timothy Tschaplinski Gerald Tuskan Environmental Sciences Division Oak Ridge National Laboratory USA Managed by UT-Battelle

2 Identification of taxon-specific genes has both scientific and practical value Conserved function New function (Common) (Unique) 2 Managed by UT-Battelle

3 Plant genome sequences Eudicot Monocot Eurosids II Eurosids I Arabidopsis Carica Medicago Glycine Populus Vitis Zea Sorghum Oryza 3 Managed by UT-Battelle

4 Objectives To identify lineage-specific genes in reference plant species To explore functions of the specific genes via expression analysis To study the evolution of the lineage-specific genes Application of the knowledge gained to bioenergy and carbon sequestration research (Candidate genes) 4 Managed by UT-Battelle

5 Approach Arabidopsis Pairwise BLASTp Populus Oryza No-hits, expressed Differential gene (DG) 594 proteins 917 proteins 2781 proteins tblast n Transcripts of plant species No-hits 150 proteins 220 proteins 699 proteins BLASTp nr protein database No-hits 109 proteins 193 proteins 653 proteins BLASTp Newly-sequenced genomes 5 Managed by UT-Battelle No-hits; Species-specific (SS) 109 proteins 192 proteins 641 proteins

6 The percentage of differential genes showing homology to other plants 6 Managed by UT-Battelle

7 Expression of the Arabidopsis SS genes Cluster01 Cluster02 Cluster03 Cluster04 Cluster05 Cluster06 Cluster07 Cluster08 Cluster09 Cluster10 Cluster11 Cluster12 Cluster13 Cluster14 Cluster15 Cluster16 Cluster17 Cluster18 Cluster19 Cluster20 Cluster21 Cluster22 Cluster23 Cluster24 7 Managed by UT-Battelle

8 Expression of the Arabidopsis SS (Cluster01) Cotyledons Hypocotyl Roots, 7d Shoot apex Roots, 17d Rosette leaf # 8 Senescing leaf 2nd internode Flowers stage 10 Flowers stage 12 sepal petal stamen carpel Flower stage 15 sepal petal stamen carpel Mature pollen Silique Seed 8 Managed by UT-Battelle

9 Expression of the Populus SS genes Cluster01 Cluster02 Cluster03 Cluster04 Cluster05 Cluster06 Cluster07 Cluster08 Cluster09 Cluster10 Cluster11 Cluster12 Cluster13 Cluster14 Cluster15 Cluster16 Cluster17 Cluster18 Cluster19 Cluster20 Cluster21 Cluster22 Cluster23 Cluster24 9 Managed by UT-Battelle

10 Expression of the Populus SS genes Cluster13 Cluster14 Cluster06 10 Managed by UT-Battelle

11 Number of introns per gene in Arabidopsis, Oryza & Populus Intron number per gene: 3-or-more introns 2 introns 1 intron 0 intron (Intronless) indicates that genes are over-represented and - under-represented at P < 1x10-5, as compared with all genes in the whole genome Managed by UT-Battelle

12 qpcr analysis of expression of Populus- specific & differential gene sets 12 Managed by UT-Battelle

13 Conserved motifs in Arabidopsis- and Oryza-specific proteins 13 Managed by UT-Battelle

14 Other species sharing motifs with Arabidopsis- and Oryza-specific genes 14 Managed by UT-Battelle

15 Summary 192, 641 and 109 species-specific specific (SS) genes were discovered in Arabidopsis, Oryza and Populus,, respectively Some SS genes were preferentially expressed in flowers, roots, xylem (and cambium or up- regulated by stress, data not shown) 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 Populus-specific genes are likely candidates for carbon sequestration & biofuel 15 Managed by UT-Battelle

16 Acknowledgements Gerald Tuskan, Sara Jawdy, Timothy Tschaplinski Stan Wullschleger, Udaya Kalluri, Lee Gunter 16 Managed by UT-Battelle