Generation-biased gene expression in a bryophyte model system

The evolution of land plants is tightly linked to the evolution of the alternation of generations. Because alternating ploidal generations share their genomes, investigating generation-biased gene expression can give insight into the evolution of life cycles in land plants. Toward this end, we describe gene expression differences associated with the alternation of isogenic sporophyte and gametophyte generations in bryophytes, extant representatives of early diverging land plants, using a moss model system (Funaria hygrometrica). We found that differentiation in gene expression between the sporophyte and gametophyte generations is weaker in the bryophyte model system than in Arabidopsis thaliana. This is in line with the basal phylogenetic position of bryophytes and with the origin of alternating generations from a purely haplontic life cycle. Comparative analysis of F. hygrometrica and A. thaliana gene expression data shows that there is limited conservation of generation-biased gene expression across land plants. However, genes showing shared sporophyte-biased expression in both F. hygrometrica and A. thaliana appear to be enriched for biological pathways representing critical molecular adaptations to terrestrial life. Comparative analyses of the expression of F. hygrometrica and A. thaliana regulatory genes suggest that conserved regulatory networks may be involved in growth and reproductive tissue development of the angiosperm and bryophyte sporophyte generations despite their morphological divergence. This study represents the first attempt to describe generation-biased gene expression in a plant with a well-developed sporophyte and gametophyte generations, and as such it lays the foundation for future targeted research on the developmental mechanisms underlying evolutionary diversification of plant sporophytes.