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Summary With global climate change, water scarcity threatens whole agro/ecosystems. The desert mossSyntrichia caninervis, an extremophile, offers novel insights into surviving desiccation and heat. The sequencedS. caninervisgenome consists of 13 chromosomes containing 16 545 protein‐coding genes and 2666 unplaced scaffolds. Syntenic relationships within theS.caninervisandPhyscomitrellapatensgenomes indicate theS. caninervisgenome has undergone a single whole genome duplication event (compared to two forP. patens) and evidence suggests chromosomal or segmental losses in the evolutionary history ofS. caninervis. The genome contains a large sex chromosome composed primarily of repetitive sequences with a large number ofCopiaandGypsyelements. Orthogroup analyses revealed an expansion ofELIPgenes encoding proteins important in photoprotection. The transcriptomic response to desiccation identified four structural clusters of novel genes. The genomic resources established for this extremophile offer new perspectives for understanding the evolution of desiccation tolerance in plants. 

Abstract Mosses (Bryophyta) are a key group occupying an important phylogenetic position in land plant (embryophyte) evolution. The class Bryopsida represents the most diversified lineage, containing more than 95% of modern mosses, whereas other classes are species‐poor. Two branches with large numbers of gene duplications were elucidated by phylogenomic analyses, one in the ancestry of all mosses and another before the separation of the Bryopsida, Polytrichopsida, and Tetraphidopsida. The analysis of the phylogenetic progression of duplicated paralogs retained on genomic syntenic regions in thePhyscomitrella patensgenome confirmed that the whole‐genome duplication events WGD1 and WGD2 were re‐recognized as the ψ event and the Funarioideae duplication event, respectively. The ψ polyploidy event was tightly associated with the early diversification of Bryopsida, in the ancestor of Bryidae, Dicranidae, Timmiidae, and Funariidae. Together, four branches with large numbers of gene duplications were unveiled in the evolutionary past ofP. patens. Gene retention patterns following the four large‐scale duplications in different moss lineages were analyzed and discussed. Recurrent significant retention of stress‐related genes may have contributed to their adaption to distinct ecological environments and the evolutionary success of this early‐diverging land plant lineage.