Figure 1.

Retrogene Identification and Genomic Features.

(A) Schematic representation of the retrogene identification method developed for our study.

(B) Venn diagrams indicating the numbers of retrogenes identified in three Arabidopsis genome-wide searches (Zhang et al., 2005; Zhu et al., 2009; this study). Note that the Venn diagrams do not include the disputable retrogenes listed in Supplemental Data Set 2.

(C) Relative abundance (y axis) of TEs (black), genes and pseudogenes (background; green), retrogenes (red), and parents (blue) over the five Arabidopsis chromosomes (x axis).

(D) Percentage of genes containing TEs (y axis) in 1-kb intervals from the gene TSS and TTS for all protein-coding genes (background; green), retrogenes (red), and parents (blue). Significant differences (P < 0.05) in the χ² test relative to background are indicated by asterisks.