Figure 3.

Retrogenes Are Transcriptionally Upregulated in Pollen.

(A) Mean gcRMA values for genome-wide genes (GW), parents (P), and retrogenes (R) at each of the 49 Arabidopsis developmental stages.

(B) Hierarchically clustered heat map of retrogene z-scores (y axis) and developmental stages (x axis).

(C) The frequency of retrogenes with row z-scores in (B) >0, >1, and >3 in individual developmental stages.

(D) Examples of retrogenes and parents showing tissue-specific and ubiquitous transcription, respectively, with major transcription changes in pollen (stage 39).

(E) Developmental gcRMA values for the genome-wide set of genes and retrogenes. Transcription is shown for mean (M) and transcription quantiles: lowly transcribed/quantile 1 (Q1), mid-lowly transcribed/quantile 2 (Q2), mid-highly transcribed/quantile 3 (Q3), and highly transcribed/quantile 4 (Q4).

(F) Mean RNA sequencing reads per kilobase per million reads (RPKM) values for all genes (genome-wide), parents, and retrogenes in vegetative rosettes and pollen as complete data sets, quantile 1 (lowly transcribed genes), and quantile 4 (highly transcribed genes).