Here, we gathered a collection of 133 accessions of the model bryophyte Marchantia polymorpha and studied its intraspecific diversity using selection signature analyses, a genome–environment association study and a pangenome.
We identified adaptive features, such as peroxidases or nucleotide-binding and leucine-rich repeats (NLRs), also observed in flowering plants, likely inherited from the first land plants. The M. polymorpha pangenome also harbors lineage-specific accessory genes absent from seed plants.
We conclude that different land plant lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage-specific polymorphisms and gene family evolution.
Following their transition from an aquatic to a terrestrial habitat, plants had already diversified in two main lineages 400 million years ago1,2,3,4,5,6: the vascular plants (tracheophytes), which include all flowering plants, and the nonvascular plants (bryophytes), which encompass hornworts, mosses and liverworts.
Following their transition from an aquatic to a terrestrial habitat, plants had already diversified in two main lineages 400 million years ago1,2,3,4,5,6: the vascular plants (tracheophytes), which include all flowering plants, and the nonvascular plants (bryophytes), which encompass hornworts, mosses and liverworts.
The long-lasting colonization of terrestrial habitats by bryophytes and tracheophytes is the result of an initial burst of innovations3,4,5,6 followed by continuous adaptations to new environments, leading to the spread of plants in most ecosystems on Earth.
The genetics of population adaptation to environmental constraints has been explored by genome–environment association (GEA) studies in crops and in nondomesticated model angiosperms7. These led to the discovery of genetic variants ranging from SNPs8 to structural and gene presence–absence variations when species pangenomes were used9,10, demonstrating the diversity of the genetic bases of adaptation in angiosperms. These approaches facilitated the identification of loci to be used as breeding or genome-editing targets for crop improvement even between species11,12,13.
The response of individual plants to environmental factors has been studied in tracheophytes and in bryophytes, leading to the discovery of transcriptomic and physiological responses to abiotic stresses14,15 and to pathogenic or mutualistic biotic interactions4,16,17,18. Combined with phylogenomics and evo–devo, these approaches revealed that part of the molecular mechanisms regulating these responses to environmental factors are highly conserved across land plants. Although lineage-specific mechanisms occur, this suggests that studying bryophytes can inform work in angiosperms, including for applied purposes.
We hypothesize that, beyond the characterized molecular mechanisms conserved in tracheophytes and bryophytes studied by evo–devo approaches, gene families might have been involved in the adaptation to environmental factors in the two groups. However, adaptive traits evolved by bryophytes over the last 450 million years19 as well as their potential conservation in other lineages have not been explored.
The genetics of population adaptation to environmental constraints has been explored by genome–environment association (GEA) studies in crops and in nondomesticated model angiosperms7. These led to the discovery of genetic variants ranging from SNPs8 to structural and gene presence–absence variations when species pangenomes were used9,10, demonstrating the diversity of the genetic bases of adaptation in angiosperms. These approaches facilitated the identification of loci to be used as breeding or genome-editing targets for crop improvement even between species11,12,13.
The response of individual plants to environmental factors has been studied in tracheophytes and in bryophytes, leading to the discovery of transcriptomic and physiological responses to abiotic stresses14,15 and to pathogenic or mutualistic biotic interactions4,16,17,18. Combined with phylogenomics and evo–devo, these approaches revealed that part of the molecular mechanisms regulating these responses to environmental factors are highly conserved across land plants. Although lineage-specific mechanisms occur, this suggests that studying bryophytes can inform work in angiosperms, including for applied purposes.
We hypothesize that, beyond the characterized molecular mechanisms conserved in tracheophytes and bryophytes studied by evo–devo approaches, gene families might have been involved in the adaptation to environmental factors in the two groups. However, adaptive traits evolved by bryophytes over the last 450 million years19 as well as their potential conservation in other lineages have not been explored.
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