MAdLandExpression: integrating sexual reproduction into the Physcomitrium patens expression atlas.
Physcomitrium patens is a bryophyte model system particularly valuable for evolutionary developmental and comparative genomics studies. Sexual reproduction in bryophytes offers unique insights into the evolution of land plant reproduction. Unlike seed plants, bryophytes have a dominant gametophyte phase and provide significant advantages for studying sexual reproduction, such as the possibility to maintain embryo-lethal mutants through vegetative propagation or the presence of motile male gametes. More than 25 years after the first publications of transcriptomic data for P. patens, expression data of most developmental stages of P. patens as well as its responses to various biotic and abiotic perturbations have been represented by microarrays or RNA-seq datasets. To facilitate the use of such data, we introduce the MAdLandExpression atlas as a successor of PEATmoss (Physcomitrium Expression Atlas Tool), integrating its 109 P. patens expression experiments and expanding it with 20 recently published RNA-seq samples of sexual reproduction stages, thus completing the coverage of the P. patens life cycle. The MAdLandExpression atlas also introduces new features for data visualization and analysis, such as the comparison of samples from multiple datasets and gene set normalization. Using this tool, the sexual reproduction dataset was analyzed, identifying genes potentially important for egg and sperm cell development, and confirming the behavior of known key genes in sexual development observed in previous studies.