The Genome of the Model Moss Physcomitrella patens

For more than two decades, the moss Physcomitrella patens has been developed and employed as a model species for comparative studies of plant biology as well as a safe production system for biotechnology. Early on, the generation and dissemination of transcriptomic and genomic resources was an important focal point of Physcomitrella research, which, together with the ease of genetic modification and flexibility of cultivation, over the years has attracted more and more research groups all around the world to use this moss as a model for basic and applied research. The establishment of genomic resources has culminated in the role of the P. patens genome as a reference genome for plant evolution. There are two main parts of this chapter: in the first part we provide an overview and history of the established genomic resources and in the second part we summarize the current biological knowledge about the genome structure, nature of nonprotein- and protein-coding genes including codon usage bias, repeats and transposable elements encoded by the Physcomitrella genome and, where applicable, discuss these attributes in an evolutionary context. Furthermore, we focus on the duplicated parts of the moss genome, like the paralogous genes that were retained after ancestral, large-scale to whole-genome duplication events and can be used to gain insights into the evolutionary history of Physcomitrella. Finally, we conclude this chapter by highlighting a special class of ancient paralogs in the Physcomitrella genome that have been actively retained as redundant copies and might act as pseudoalleles