Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification

American Journal of Botany, Journal Year: 2023, Volume and Issue: 110(11)

Published: Oct. 4, 2023

Abstract Premise Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding the evolutionary history hornworts, liverworts, and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy various traits repeated bursts diversification. However, timing key events phylogeny, patterns, processes diversification across bryophytes remain unclear. Methods Using GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species 52 54 orders bryophytes. We inferred phylogeny gene tree analyses using concatenated coalescence approaches, assessed conflict, estimated divergences based on 29 fossil calibrations. Results The resolves many relationships bryophytes, enabling us to resurrect five liverwort recognize three more propose 10 new mosses. Most originated Jurassic diversified Cretaceous or later. phylogenomic data also highlight topological conflict parts tree, suggesting complex that cannot be adequately captured single gene‐tree topology. Conclusions sampled hundreds loci broad phylogenetic spectrum spanning at least 450 Ma evolution; these resolved critical nodes need explore mechanisms underlying ambiguity specific nodes. provide an expandable framework toward reconstructing comprehensive this important group plants.

Language: Английский

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Reflections on the ABC model of flower development

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(5), P. 1334 - 1357

Published: Feb. 12, 2024

Abstract The formulation of the ABC model by a handful pioneer plant developmental geneticists was seminal event in quest to answer seemingly simple question: how are flowers formed? Fast forward 30 years and this elegant has generated vibrant diverse community, capturing imagination evolutionary biologists, structuralists, biochemists molecular biologists alike. Together they have managed solve many floral mysteries, uncovering regulatory processes that generate characteristic spatio-temporal expression patterns homeotic genes, elucidating some mechanisms allowing genes specify distinct organ identities, revealing evolution tinkers with morphological diversity, even shining light on origins gene network itself. Here we retrace history model, from its genesis current form, highlighting specific milestones along way before drawing attention unsolved riddles still hidden alphabet.

Language: Английский

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Evolution of the jasmonate ligands and their biosynthetic pathways

New Phytologist, Journal Year: 2023, Volume and Issue: 238(5), P. 2236 - 2246

Published: March 21, 2023

Different plant species employ different jasmonates to activate a conserved signalling pathway in land plants, where (+)-7-iso-JA-Ile (JA-Ile) is the ligand for COI1/JAZ receptor angiosperms and dn-cis-OPDA, dn-iso-OPDA Δ4 -dn-iso-OPDA act as ligands Marchantia polymorpha. In addition, some play COI1-independent role. To understand distribution of bioactive green lineage how their biosynthetic pathways evolved, we performed phylogenetic analyses systematic profiling representative from lineages. We found that both OPDA dn-OPDA are ubiquitous all tested plants present also charophyte algae, underscoring importance ancestral molecules. By contrast, JA-Ile biosynthesis emerged within lycophytes coincident with evolutionary appearance JAR1 function. identified OPR3-independent JA ancient predates OPR3-dependent pathway. Moreover, negative correlation between which supports bryophytes represents analogous hormone other vascular plants.

Language: Английский

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Jasmonates and salicylic acid: Evolution of defense hormones in land plants

Current Opinion in Plant Biology, Journal Year: 2023, Volume and Issue: 76, P. 102470 - 102470

Published: Oct. 4, 2023

The emergence of plant hormone signaling pathways is deeply intertwined with land evolution. In angiosperms, two hormones, salicylic Acid (SA) and Jasmonates (JAs), play a key role in defense, where JAs-mediated defenses are typically activated response to herbivores necrotrophic pathogens, whereas SA prioritized against hemi/biotrophic pathogens. Thus, studying the evolution JAs their crosstalk essential understand molecular plant-microbe interactions (EvoMPMI) plants. Recent advances biosynthesis, signaling, plants illustrated that insight gained angiosperms does not necessarily apply non-seed lineages, receptors perceive different ligands hormones activate independently on canonical receptors. this review, recent findings main defense (JAs SA) plants, including functional studies bryophyte model Marchantia polymorpha, will be discussed.

Language: Английский

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Green land: Multiple perspectives on green algal evolution and the earliest land plants

American Journal of Botany, Journal Year: 2023, Volume and Issue: 110(5)

Published: May 1, 2023

Green plants, broadly defined as green algae and the land plants (together, Viridiplantae), constitute primary eukaryotic lineage that successfully colonized Earth's emergent landscape. Members of various clades have independently made transition from fully aquatic to subaerial habitats many times throughout history. The transition, unicells or simple filaments complex multicellular plant bodies with functionally differentiated tissues organs, was accompanied by innovations built upon a genetic phenotypic toolkit served phototrophs for at least billion years. These opened an enormous array new, drier places live on planet resulted in huge diversity dominated terrestrial ecosystems over past 500 million This review examines greening several perspectives, paleontology phylogenomics, water stress responses shared genomic evolution sporophyte generation. We summarize advances disparate fronts elucidating this important event biosphere lacunae our understanding it. present process not step-by-step advancement primitive cells inevitable success embryophytes, but rather adaptations exaptations allowed multiple combinations morphological physiological terrestrialized traits, become diverse successful inhabitants Earth.

Language: Английский

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Phytohormones in a universe of regulatory metabolites: lessons from jasmonate

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(1), P. 135 - 154

Published: Jan. 30, 2024

Small-molecule phytohormones exert control over plant growth, development, and stress responses by coordinating the patterns of gene expression within between cells. Increasing evidence indicates that currently recognized hormones are part a larger group regulatory metabolites have acquired signaling properties during evolution land plants. This rich assortment chemical signals reflects tremendous diversity secondary metabolism, which offers evolutionary solutions to daunting challenges sessility other unique aspects biology. A major gap in our current understanding is lack insight into direct targets these compounds. Here, we illustrate blurred distinction classical bioactive highlighting scientific advances transformed view jasmonate from an interesting floral scent potent transcriptional regulator. Lessons research generally apply thus may help provide broad metabolite-protein interactions. In providing framework links small-molecule plasticity, hope stimulate future explore evolution, functions, mechanisms perception range metabolites.

Language: Английский

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The landscape of transcription factor promoter activity during vegetative development in Marchantia

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(6), P. 2140 - 2159

Published: Feb. 23, 2024

Abstract Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterizing transcriptional activity TF genes in space time is a critical step toward understanding complex biological systems. The vegetative gametophyte meristems bryophytes share some characteristics with shoot apical flowering plants. However, identity profiles TFs associated organization largely unknown. With only ∼450 putative genes, Marchantia (Marchantia polymorpha) an outstanding model system plant systems biology. We have generated near-complete collection promoter elements derived from genes. experimentally tested reporter fusions all promoters systematically analyzed patterns gemmae. This allowed us to build map domains early development identify set TF-derived that active stem-cell zone. markers provide additional tools insight into dynamic gametophytic meristem its evolution. In addition, we online database collection. expect these will be useful cell-type-specific expression, synthetic biology applications, functional genomics.

Language: Английский

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Land plant peptide signaling: What we know—and don't know—about its evolution

Physiologia Plantarum, Journal Year: 2024, Volume and Issue: 176(1)

Published: Jan. 1, 2024

Abstract The availability of genome sequences from diverse algal and plant taxa combined with the refinement comparative genomics tools has begun to reveal how land genomes were shaped through duplication, repeat expansion, gene family gains losses. Of particular note is a large increase in complexity variety signaling systems plants. Among these, small peptide ligand‐receptor interactions been considered one major innovations during evolution. First discovered angiosperms as mediators various cell‐to‐cell communication processes, studies have expanded non‐angiosperms, including bryophytes. Recent point both common unique roles for distantly related species, raising interesting questions about evolved diversified. While origin remains elusive, progress sequencing offers clues understanding evolution receptors. This article discusses recent peptide‐mediated highlights current gaps our knowledge new avenues research, which could help us address contributed terrestrialization.

Language: Английский

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The role of indole‐3‐acetic acid and characterization of PIN transporters in complex streptophyte alga Chara braunii

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 6, 2025

Auxin, indole-3-acetic acid (IAA), is a key phytohormone with diverse morphogenic roles in land plants, but its function and transport mechanisms algae remain poorly understood. We therefore aimed to explore the role of IAA complex, streptophyte Chara braunii. Here, we described novel responses C. braunii characterized two homologs PIN auxin efflux carriers: CbPINa CbPINc. determined their localization using epitope-specific antibodies tested heterologous plant models. Further, phosphoproteomic analysis, identified IAA-induced phosphorylation events. The thallus regeneration assay showed that promotes elongation side branch development. Immunolocalization CbPINc confirmed presence on plasma membrane vegetative generative cells However, functional assays tobacco BY-2 demonstrated affects transport, whereas does not. effective acceleration cytoplasmic streaming evolutionary conserved targets such as homolog RAF-like kinase. These findings suggest that, although canonical PIN-mediated might not be fully Chara, involved morphogenesis fast signaling processes.

Language: Английский

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The maturation and aging trajectory of Marchantia polymorpha at single-cell resolution

Developmental Cell, Journal Year: 2023, Volume and Issue: 58(15), P. 1429 - 1444.e6

Published: June 15, 2023

Bryophytes represents a sister to the rest of land plants. Despite their evolutionary importance and relatively simple body plan, comprehensive understanding cell types transcriptional states that underpin temporal development bryophytes has not been achieved. Using time-resolved single-cell RNA sequencing, we define cellular taxonomy Marchantia polymorpha across asexual reproduction phases. We identify two maturation aging trajectories main plant M. at resolution: gradual tissues organs along tip-to-base axis midvein progressive decline meristem activities in tip chronological axis. Specifically, observe latter is temporally correlated with formation clonal propagules, suggesting an ancient strategy optimize allocation resources producing offspring. Our work thus provides insights into heterogeneity underpins bryophytes.

Language: Английский

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