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

---

Pan-phylum genomes of hornworts reveal conserved autosomes but dynamic accessory and sex chromosomes

Nature Plants, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Language: Английский

---

The Bryophyte Phylogeny Group: A revised familial classification system based on plastid phylogenomic data

Journal of Systematics and Evolution, Journal Year: 2024, Volume and Issue: 62(4), P. 577 - 588

Published: March 12, 2024

Abstract Bryophytes, a monophyletic group comprising three major lineages, diversified soon after the terrestrialization of land plants. However, their internal phylogenetic relationships remain controversial. In this study, we reconstructed ordinal and familial phylogeny bryophytes using largest plastid data set to date, including 549 taxa that represent almost all known orders two‐thirds families. The strongly supported inference enabled us propose in mosses seven newly segregated families, is, Baldwiniellaceae, Calyptrochaetaceae, Ctenidiaceae, Herpetineuraceae, Isodrepaniaceae, Pseudotaxiphyllaceae, Rozeaceae, one reduced family, Climaciaceae. We also transferred liverwort family Calyculariaceae from Fossombroniales Pelliales. Recent advancements molecular have revolutionized bryophyte classification, tending be more fragmental. Hence, further revised classification system for includes 45 142 families mosses, 23 85 liverworts, five hornworts.

Language: Английский

---

Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.)

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: Jan. 15, 2025

Abstract Riccia sorocarpa Bisch., commonly known as common crystalwort, is a plant belonging to the Marchantiales order with cosmopolitan distribution among wide range of habitats: fields, gardens, waste ground, on paths, cliff tops, and thin soil over rocks or by water bodies. However, research into genetic aspects this species limited. In study, chromosome-scale telomere-to-telomere genome R. was assembled exclusively Oxford Nanopore long-read sequencing Pore-C technology. A high-quality chromosomal-scale assembly obtained final size 376.690 Mbp, contig N50 49.132 Mbp 97.02% contigs associated eight chromosomes. Genome completeness confirmed BUSCO analysis accounting 91.8%. Among 27,626 total genes, 23,562 (85.29%) were functionally annotated. Moreover, collinearity analyzed well gene family evolution DNA methylation profile. The availability genome, which second liverwort assembly, opens up new avenues for in-depth diversity genomic characteristics.

Language: Английский

---

Callose in leptoid cell walls of the moss Polytrichum and the evolution of callose synthase across bryophytes

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Feb. 7, 2024

Introduction Leptoids, the food-conducting cells of polytrichaceous mosses, share key structural features with sieve elements in tracheophytes, including an elongated shape oblique end walls containing modified plasmodesmata or pores. In callose is instrumental developing pores that enable efficient photoassimilate transport. Aside from a few studies using aniline blue fluorescence yielded confusing results, little known about moss leptoids. Methods Callose location and abundance during development leptoid cell was investigated Polytrichum commune quantitative immunogold labeling (label density) transmission electron microscope. To evaluate changes abiotic stress, leptoids hydrated plants compared to dried for 14 days under field conditions. A bioinformatic study assess evolution within across bryophytes conducted synthase (CalS) genes 46 (24 15 liverworts, 7 hornworts) one representative each five tracheophyte groups. Results increases around meristematic mature Controlled drying resulted significant increase label density over counts plants. Phylogenetic analysis CalS protein family recovered main clades (A, B, C). Different where greatest diversity homologs found clade A, majority gene duplication B. Discussion This work identifies as crucial wall polymer their inception functioning leptoids, water stress similar tracheophytes. Among bryophytes, mosses exhibit number multiple events, while only two duplications are revealed hornwort none liverworts. The absence essential pore angiosperms, reveals different responsible synthesizing associated mosses.

Language: Английский

---

Biolistics-mediated transformation of hornworts and its application to study pyrenoid protein localization

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(16), P. 4760 - 4771

Published: May 23, 2024

Hornworts are a deeply diverged lineage of bryophytes and sister to mosses liverworts. have an array unique features that can be leveraged illuminate not only the early evolution land plants, but also alternative paths for nitrogen carbon assimilation via cyanobacterial symbiosis pyrenoid-based CO2-concentrating mechanism (CCM), respectively. Despite this, hornworts one few plant lineages with limited available genetic tools. Here we report efficient biolistics method generating transient expression stable transgenic lines in model hornwort, Anthoceros agrestis. An average 569 (±268) cells showed per bombardment, green fluorescent protein observed within 48-72 h. A total 81 stably transformed were recovered across three separate experiments, averaging six bombardment. We followed same transiently transform nine additional hornwort species, obtained transformants from one. This was further used verify localization Rubisco activase pyrenoids, which central proteins CCM function. Together, our approach offers key advantages over existing methods as it enables rapid applied widely diverse species.

Language: Английский

---

Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(7)

Published: May 23, 2024

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, 414 Mb comprises 26 chromosomes 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This holds 2 that withstood rigorous filtration microbial contaminants, have no homolog in other land plants, are thus interpreted as resulting unique horizontal gene transfers (HGTs) microbes. Further, P. shares 176 273 published HGT candidates identified Physcomitrium patens patens), but lacks 98 these, highlighting perhaps many 91 were acquired last 40 million years following its divergence common ancestor with africana. These observations suggest rather continuous gains via followed by potential losses during diversification Funariaceae. Our findings showcase both dynamic flux plant HGTs over evolutionarily "short" timescales, alongside enduring impacts successful integrations, like those still functionally maintained extant Furthermore, this study describes informatic processes employed to distinguish contaminants candidate events.

Language: Английский

---

Lineages of Fractal Genera Comprise the 88-Million-Year Steel Evolutionary Spine of the Ecosphere

Plants, Journal Year: 2024, Volume and Issue: 13(11), P. 1559 - 1559

Published: June 5, 2024

Fractal evolution is apparently effective in selectively preserving environmentally resilient traits for more than 80 million years Streptotrichaceae (Bryophyta). An analysis simulated maximum destruction of ancestral that large lineage. The constraints enforced were the preservation newest traits, and all immediate descendant species obtained different new traits. Maximum character state changes 16 percent possible any one sub-lineage, or 73 total entire Results showed, however, only four permanently eliminated lineage sub-lineage. A maintains biodiversity temporally regionally survival-effective at minimum expense to resilience across a geologic time 88 group studied. Similar processes generating an extant punctuated equilibrium as bursts about descendants per genus 1–2 epochs are other living groups given similar emergent processes. mechanism considered complexity-related, being self-organized phenomenon strongly maintained ecosphere by natural selection on fractal genera.

Language: Английский

---

Overlooked and misunderstood: A morpho‐molecular revision of Ditrichaceae s.str. (Dicranidae, Bryophyta), with a focus on the Holarctic species of Ditrichum

Taxon, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 12, 2025

Abstract We revised the Holarctic taxa of Ditrichaceae on basis both organellar DNA sequence data and morphological traits. After removal phylogenetically discordant elements related to Flexitrichum Rhamphidium , remaining representatives family cluster into three well‐supported lineages, which are recognized here as reinstated Ceratodontaceae a more restricted with two subfamilies. is segregated newly described family, Rhamphidiaceae; Aongstroemia gayana Dicranella vaginata Symblepharis krausei combined under genus Strombulidens tentatively moved Rhamphidiaceae. includes genera Ceratodon Cheilothela Trichodon Pseudaongstroemia single species, known earlier fuji‐alpina . The paraphyletically defined include T. cylindricus oblongus at specific rank, molecularly distinct lineage, we were unable distinguish morphologically from monoicous autoicous Ditrichum previously understood merged genus, Pleuridium subfam. Pleuridioideae stat. nov. A also accepted within Ditrichoideae, following transfer julacea s.str. A. orientalis septentrionale based material mostly North Asia. Two ecologically specialized, putatively only locally distributed synonymized widespread taxa. plumbicola placed synonymy D. lineare similarly cornubicum macrorhynchum delimitations pusillum clarified emended.

Language: Английский

---

Extending the fossil record of Miocene neotropical epiphyte communities

Fossil record, Journal Year: 2025, Volume and Issue: 28(1), P. 79 - 102

Published: Feb. 27, 2025

Dominican amber (15–20 Ma) and Mexican (15–23 are valuable sources of fossil epiphytic bryophytes, ferns, lichens. Both ambers derive from resins Hymenaea , a genus in the Fabaceae family still occurring Mexico, Central America, Caribbean today. The inclusions provide rare glimpses into Miocene neotropical epiphyte communities life-like preservation. In this study, we extend record these describe Frullania chiapasensis Thysananthus patrickmuelleri two new species leafy liverworts amber. is fourth representative tropical rather diverse amber, it here newly recorded Additionally, treat five fossils at level, including one liverwort ( Lejeunea sp.) as well three lichens lichen all belonging to extant Parmotrema . All four cryptogamic genera common elements subtropical forests. evidence substantiates that were very similar ones generic level.

Language: Английский

---