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1. Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants

   https://doi.org/10.1093/molbev/msab106  

   Su, Danyan; Yang, Lingxiao; Shi, Xuan; Ma, Xiaoya; Zhou, Xiaofan; Hedges, S Blair; Zhong, Bojian (April 2021, Molecular Biology and Evolution)

   Battistuzzi, Fabia Ursula (Ed.)

   Abstract The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980–682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny. 

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2. The hornworts: morphology, evolution and development

   https://doi.org/10.1111/nph.16874  

   Frangedakis, Eftychios; Shimamura, Masaki; Villarreal, Juan Carlos; Li, Fay‐Wei; Tomaselli, Marta; Waller, Manuel; Sakakibara, Keiko; Renzaglia, Karen S.; Szövényi, Péter (September 2020, New Phytologist)

   Summary Extant land plants consist of two deeply divergent groups, tracheophytes and bryophytes, which shared a common ancestor some 500 million years ago. While information about vascular plants and the two of the three lineages of bryophytes, the mosses and liverworts, is steadily accumulating, the biology of hornworts remains poorly explored. Yet, as the sister group to liverworts and mosses, hornworts are critical in understanding the evolution of key land plant traits. Until recently, there was no hornwort model species amenable to systematic experimental investigation, which hampered detailed insight into the molecular biology and genetics of this unique group of land plants. The emerging hornwort model species,Anthoceros agrestis, is instrumental in our efforts to better understand not only hornwort biology but also fundamental questions of land plant evolution. To this end, here we provide an overview of hornwort biology and current research on the model plantA. agrestisto highlight its potential in answering key questions of land plant biology and evolution. 

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3. The ancestral chromatin landscape of land plants

   https://doi.org/10.1111/nph.19311  

   Hisanaga, Tetsuya; Wu, Shuangyang; Schafran, Peter; Axelsson, Elin; Akimcheva, Svetlana; Dolan, Liam; Li, Fay‐Wei; Berger, Frédéric (October 2023, New Phytologist)

   Summary Recent studies have shown that correlations between chromatin modifications and transcription vary among eukaryotes. This is the case for marked differences between the chromatin of the mossPhyscomitrium patensand the liverwortMarchantia polymorpha. Mosses and liverworts diverged from hornworts, altogether forming the lineage of bryophytes that shared a common ancestor with land plants. We aimed to describe chromatin in hornworts to establish synapomorphies across bryophytes and approach a definition of the ancestral chromatin organization of land plants.We used genomic methods to define the 3D organization of chromatin and map the chromatin landscape of the model hornwortAnthoceros agrestis.We report that nearly half of the hornwort transposons were associated with facultative heterochromatin and euchromatin and formed the center of topologically associated domains delimited by protein coding genes. Transposons were scattered across autosomes, which contrasted with the dense compartments of constitutive heterochromatin surrounding the centromeres in flowering plants.Most of the features observed in hornworts are also present in liverworts or in mosses but are distinct from flowering plants. Hence, the ancestral genome of bryophytes was likely a patchwork of units of euchromatin interspersed within facultative and constitutive heterochromatin. We propose this genome organization was ancestral to land plants. 

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4. Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages

   https://doi.org/10.1093/gbe/evac183  

   Timilsena, Prakash Raj; Barrett, Craig F; Piñeyro-Nelson, Alma; Wafula, Eric K; Ayyampalayam, Saravanaraj; McNeal, Joel R; Yukawa, Tomohisa; Givnish, Thomas J; Graham, Sean W; Pires, J Chris; et al (January 2023, Genome Biology and Evolution)

   Mayrose, Itay (Ed.)

   Abstract Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have evolved repeatedly in plants, particularly in monocots. Although reductive evolution of plastomes in mycoheterotrophs is well documented, the dynamics of nuclear genome evolution remains largely unknown. Transcriptome datasets were generated from four mycoheterotrophs in three families (Orchidaceae, Burmanniaceae, Triuridaceae) and related green plants and used for phylogenomic analyses to resolve relationships among the mycoheterotrophs, their relatives, and representatives across the monocots. Phylogenetic trees based on 602 genes were mostly congruent with plastome phylogenies, except for an Asparagales + Liliales clade inferred in the nuclear trees. Reduction and loss of chlorophyll synthesis and photosynthetic gene expression and relaxation of purifying selection on retained genes were progressive, with greater loss in older nonphotosynthetic lineages. One hundred seventy-four of 1375 plant benchmark universally conserved orthologous genes were undetected in any mycoheterotroph transcriptome or the genome of the mycoheterotrophic orchid Gastrodia but were expressed in green relatives, providing evidence for massively convergent gene loss in nonphotosynthetic lineages. We designate this set of deleted or undetected genes Missing in Mycoheterotrophs (MIM). MIM genes encode not only mainly photosynthetic or plastid membrane proteins but also a diverse set of plastid processes, genes of unknown function, mitochondrial, and cellular processes. Transcription of a photosystem II gene (psb29) in all lineages implies a nonphotosynthetic function for this and other genes retained in mycoheterotrophs. Nonphotosynthetic plants enable novel insights into gene function as well as gene expression shifts, gene loss, and convergence in nuclear genomes. 

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5. Bryophytes in fir waves: Forest canopy indicator species and functional diversity decline in canopy gaps

   https://doi.org/10.1111/jvs.12718  

   Berdugo, Monica B.; Dovciak, Martin; Nakashizuka, ed., Tohru (March 2019, Journal of Vegetation Science)

   Abstract AimsBryophytes can cover three quarters of the ground surface, play key ecological functions, and increase biodiversity in mesic high‐elevation conifer forests of the temperate zone. Forest gaps affect species coexistence (and ecosystem functions) as suggested by the gap and gap‐size partitioning hypotheses (GPH,G_SPH). Here we test these hypotheses in the context of high‐elevation forest bryophyte communities and their functional attributes. Study SiteSpruce–fir forests on Whiteface Mountain, NY,USA. MethodsWe characterized canopy openness, microclimate, forest floor substrates, vascular vegetation cover, and moss layer (cover, common species, and functional attributes) in three canopy openness environments (gap, gap edge, forest canopy) across 20 gaps (fir waves) (n = 60); the functional attributes were based on 16 morphologic, reproductive, and ecological bryophyte plant functional traits (PFTs). We testedGPHandG_SPHrelative to bryophyte community metrics (cover, composition), traits, and trait functional sensitivity (functional dispersion;FDis) using indicator species analysis, ordination, and regression. ResultsCanopy openness drove gradients in ground‐level temperature, substrate abundance and heterogeneity (beta diversity), and understory vascular vegetation cover. TheGPHwas consistent with (a) the abundance patterns of forest canopy indicator species (Dicranum fuscescens,Hypnum imponens, andTetraphis pellucida), and (b)FDisbased on threePFTs (growth form, fertility, and acidity), both increasing with canopy cover. We did not find support forGPHin the remaining species or traits, or forG_SPHin general; gap width (12–44 m) was not related to environmental or bryophyte community gradients. ConclusionsThe observed lack of variation in most bryophyte metrics across canopy environments suggests high resistance of the bryophyte layer to natural canopy gaps in high‐elevation forests. However, responses of forest canopy indicator species suggest that canopy mortality, potentially increased by changing climate or insect pests, may cause declines in some forest canopy species and consequently in the functional diversity of bryophyte communities. 

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