Genome-Wide Characterization of Wholly Disordered Proteins in Arabidopsis DOI Open Access
William J. Long, Liang Zhao, Huimin Yang

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(3), P. 1117 - 1117

Published: Jan. 28, 2025

Intrinsically disordered proteins (IDPs) include two types of proteins: partial regions (IDRs) and wholly (WDPs). Extensive studies focused on the with IDRs, but less is known about WDPs because their difficult-to-form folded tertiary structure. In this study, we developed a bioinformatics method for screening more than 50 amino acids in genome level found total 27 categories, including 56 WDPs, Arabidopsis. After comparing randomly selected structural proteins, that possessed wide range theoretical isoelectric point (PI), negative Grand Average Hydropathicity (GRAVY), higher value Instability Index (II), lower values Aliphatic (AI). addition, by calculating FCR (fraction charged residue) NCPR (net charge per each WDP, 20 R1 (FCR < 0.25 0.25) group, 15 R2 (0.25 ≤ 0.35 0.35), 19 R3 > R4 0.35). Moreover, gene expression protein-protein interaction (PPI) network analysis showed perform different biological functions. We also SIS (Salt Induced Serine rich) RAB18 (a dehydrin family protein), undergo vitro liquid-liquid phase separation (LLPS). Therefore, our results provide insight into understanding biochemical characters functions plants.

Language: Английский

Genomes of multicellular algal sisters to land plants illuminate signaling network evolution DOI Creative Commons

Xuehuan Feng,

Jinfang Zheng, Iker Irisarri

et al.

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(5), P. 1018 - 1031

Published: May 1, 2024

Abstract Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains Zygnema circumcarinatum . We inferred traits in ancestor and plants that might have ushered conquest by plants: expanded genes signaling cascades, environmental response, multicellular growth. share all major enzymes cell wall synthesis remodifications, gene gains shaped this toolkit. Co-expression network analyses uncover cohorts unite with developmental programs. Our data shed light on a molecular chassis balances response growth modulation across more than 600 million years streptophyte evolution.

Language: Английский

Citations

48
Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification DOI Creative Commons
Julia Bechteler, Gabriel F. Peñaloza‐Bojacá, David Bell

et al.

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

Citations

45
Cryogenian Origins of Multicellularity in Archaeplastida DOI Creative Commons
Alexander M. C. Bowles, Christopher J. Williamson, Tom A. Williams

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(2)

Published: Feb. 1, 2024

Abstract Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked explain both origins of multicellularity in Archaeplastida and radiation first land plants. However, temporal relationship between these environmental biological is poorly established, due a paucity molecular fossil data, precluding resolution phylogeny timescale archaeplastid evolution. We infer time-calibrated early evolution based on revised dataset reappraisal record. Phylogenetic topology testing resolves deep relationships, identifying two clades Viridiplantae placing Bryopsidales as sister Chlorophyceae. Our clock analysis infers an origin late-Paleoproterozoic early-Mesoproterozoic (1712 1387 Ma). Ancestral state reconstruction cytomorphological traits this tree reveals many independent span Cryogenian, consistent with hypothesis. Multicellular rhodophytes emerged 902 655 Ma while crown-Anydrophyta (Zygnematophyceae Embryophyta) originated 796 671 Ma, broadly compatible plant terrestrialization analyses resolve timetree age estimates for ancestral multicellular archaeplastids coinciding hypotheses that propose role Snowball

Language: Английский

Citations

17
Pan-phylum genomes of hornworts reveal conserved autosomes but dynamic accessory and sex chromosomes DOI
Peter Schafran,

Duncan A. Hauser,

Jessica Nelson

et al.

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

Published: Jan. 3, 2025

Language: Английский

Citations

3
ATP synthase evolution on a cross-braced dated tree of life DOI Creative Commons
Tara Mahendrarajah, Edmund R. R. Moody, Dominik Schrempf

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 17, 2023

Abstract The timing of early cellular evolution, from the divergence Archaea and Bacteria to origin eukaryotes, is poorly constrained. ATP synthase complex thought have originated prior Last Universal Common Ancestor (LUCA) analyses genes, together with ribosomes, played a key role in inferring rooting tree life. We reconstruct evolutionary history synthases using an expanded taxon sampling set develop phylogenetic cross-bracing approach, constraining equivalent speciation nodes be contemporaneous, based on imprint endosymbioses ancient gene duplications. This approach results highly resolved, dated species establishes absolute timeline for evolution. Our show that into F- A/V-type lineages was very event evolution dating back more than 4 Ga, potentially predating diversification Bacteria. cross-braced, life also provides insight recent transitions including eukaryogenesis, showing eukaryotic nuclear mitochondrial diverged their closest archaeal (2.67-2.19 Ga) bacterial (2.58-2.12 relatives at approximately same time, slightly longer stem-lineage.

Language: Английский

Citations

41
Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet DOI Open Access
Ruoyang Hu, Xuedong Li, Yong Hu

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(17), P. 3558 - 3576.e17

Published: Aug. 1, 2023

Language: Английский

Citations

34
The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes DOI Creative Commons
Tetsuya Hisanaga, Facundo Romani, Shuangyang Wu

et al.

Current Biology, Journal Year: 2023, Volume and Issue: 33(20), P. 4367 - 4380.e9

Published: Sept. 21, 2023

The mobility of transposable elements (TEs) contributes to evolution genomes. Their uncontrolled activity causes genomic instability; therefore, expression TEs is silenced by host are marked with DNA and H3K9 methylation, which associated silencing in flowering plants, animals, fungi. However, distantly related groups eukaryotes, H3K27me3 deposited the Polycomb repressive complex 2 (PRC2), an epigenetic mark gene plants animals. direct PRC2 has so far only been shown one species ciliates. To test if silences a broader range we generated mutants reduced analyzed role extant along lineage Archaeplastida diatom P. tricornutum. In this red alga C. merolae, greater proportion than genes were repressed PRC2, whereas bryophytes. contained potential cis-elements recognized transcription factors neighbor as transcriptional units PRC2. Thus, observed not but also diatoms ciliates, suggesting that silence last common ancestor eukaryotes. We hypothesize during Archaeplastida, TE fragments selected shape regulation, controlling networks regulated

Language: Английский

Citations

30
Green land: Multiple perspectives on green algal evolution and the earliest land plants DOI Open Access
Richard M. McCourt, Louise A. Lewis, Paul K. Strother

et al.

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

Citations

29
Genome evolution in plants and the origins of innovation DOI Creative Commons
James Clark

New Phytologist, Journal Year: 2023, Volume and Issue: 240(6), P. 2204 - 2209

Published: Sept. 2, 2023

Summary Plant evolution has been characterised by a series of major novelties in their vegetative and reproductive traits that have led to greater complexity. Underpinning this diversification the genome. When viewed at scale plant kingdom, genome punctuated conspicuous instances gene whole‐genome duplication, horizontal transfer extensive loss. The periods dynamic often coincide with key traits, demonstrating coevolution genomes phenotypes macroevolutionary scale. Conventionally, complexity diversity considered through lens duplication role loss remains comparatively unexplored. However, light reductive across multiple lineages, association between phenotypic warrants attention.

Language: Английский

Citations

25
Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.) DOI Creative Commons
Katarzyna Krawczyk, Joanna Szablińska–Piernik, Łukasz Paukszto

et al.

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

Citations

1