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Abstract

Rich ecotype collections are used for several plant models to unravel the molecular causes of phenotypicdifferences, and to investigate the effects of environmental adaption and acclimation. For the model mossPhyscomitrella patens collections of accessions are available, and have been used for phylogenetic and taxo-nomic studies, for example, but few have been investigated further for phenotypic differences. Here, wefocus on the Reute accession and provide expression profiling and comparative developmental data for sev-eral stages of sporophyte development, as well as information on genetic variation via genomic sequencing.We analysed cross-technology and cross-laboratory data to define a confident set of 15 mature sporophyte-specific genes. We find that the standard laboratory strain Gransden produces fewer sporophytes thanReute or Villersexel, although gametangia develop with the same time course and do not show evidentmorphological differences. Reute exhibits less genetic variation relative to Gransden than Villersexel, yet wefound variation between Gransden and Reute in the expression profiles of several genes, as well as variationhot spots and genes that appear to evolve under positive Darwinian selection. We analyzed expression dif-ferences between the ecotypes for selected candidate genes in the GRAS transcription factor family, thechalcone synthase family and in genes involved in cell wall modification that are potentially related to phe-notypic differences. We confirm that Reute is a P. patens ecotype, and suggest its use for reverse-geneticsstudies that involve progression through the life cycle and multiple generations.