The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.

Cell Biology and Plant Biochemistry University of Regensburg Regensburg Germany

Department of Genetics and Genome Biology University of Leicester Leicester UK

Department of Molecular Biology Cell Biology and Biochemistry Brown University Providence RI USA

Department of Plant and Soil Sciences University of Kentucky Lexington KY USA

Gregor Mendel Institute Vienna Austria

Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Oeiras Portugal

Instituto Gulbenkian de Ciência Oeiras Portugal

Laboratory of Molecular Bacteriology Department of Microbiology and Immunology Rega Institute KU Leuven Leuven Belgium

Laboratory of Pollen Biology Institute of Experimental Botany of the Czech Academy of Sciences Prague Czech Republic

Max Planck Institute for Molecular Plant Physiology Potsdam Golm Germany

School of Biological Sciences Nanyang Technological University Singapore Singapore

School of Life Sciences Gibbet Hill Campus The University of Warwick Coventry UK

VIB Center for Microbiology Leuven Belgium

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