Transcriptomes of plant gametophytes have a higher proportion of rapidly evolving and young genes than sporophytes

Reproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterise evolutionary patterns of genome wide gene expression in reproductive tissues and to compare them to developmental stages of the sporophyte, we analysed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species, Arabidopsis thaliana, rice (Oryza sativa) and soybean (Glycine max). In all three species a significant shift in gene expression occurs during gametogenesis in which genes of younger evolutionary age and higher genetic diversity contribute significantly more to the transcriptome than in other stages. We refer to this phenomenon as \"evolutionary bulge\" during plant reproductive development because it differentiates the gametophyte from the sporophyte. The extent of the bulge pattern is much stronger than the transcriptomic hourglass, which postulates that during early embryo development an increased proportion of ancient and conserved genes contribute to the total transcriptome. In the three plant species, we observed an hourglass pattern only in A. thaliana but not in rice or soybean, which suggests that unlike the evolutionary bulge of reproductive genes the transcriptomic hourglass is not a general pattern of plant embryogenesis, which is consistent with the absence of a morphologically defined phylotypic stage in plant development.