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Abstract The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily “short” timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events. 

Abstract Traits of the spore‐bearing generation have historically provided the basis for systematic concepts across the phylogenetic spectrum and depth of mosses. Whether taxa characterized by a simple sporophytic architecture are closely related or emerged from independent reduction is often ambiguous. Phylogenomic inferences in the Funariaceae, which hold the model taxonPhyscomitrium patens, revealed that several such shifts in sporophyte complexity occurred, and mostly within theEntosthodon‐Physcomitriumcomplex. Here, we report the rediscovery of the monospecific, Himalayan endemic generaBrachymeniopsisandClavitheca, after nearly 100 years and 40 years since their respective descriptions. The genera are characterized by, among other traits, their short sporophytes lacking the sporangial peristome teeth controlling spore dispersal. Phylogenomic inferences reveal thatBrachymeniopsis gymnostomaarose within the clade ofEntosthodons.str., a genus with typically long‐exserted capsules. We therefore propose to transferB. gymnostomato the genusEntosthodon, asE. gymnostomuscomb. nov.Furthermore,Clavitheca poeltii, the sole species of the genus, is morphologically highly similar toE. gymnostomus, and should also be transferred toEntosthodon, but is retained as a distinct taxon,E. poeltiicomb. nov., until additional populations allow for testing the robustness of the observed divergence in costa and seta length between the Nepalese and Chinese populations.