Species‐tree topology impacts the inference of ancient whole‐genome duplications across the angiosperm phylogeny

American Journal of Botany, Journal Year: 2024, Volume and Issue: 111(8)

Published: July 22, 2024

Abstract Premise The history of angiosperms is marked by repeated rounds ancient whole‐genome duplications (WGDs). Here we used state‐of‐the‐art methods to provide an up‐to‐date view the distribution WGDs in that considers both uncertainty introduced different WGD inference and underlying species‐tree hypotheses. Methods We synonymous divergences ( K s ) paralogs orthologs from transcriptomic genomic data infer place across two hypothesized angiosperm phylogenies. further tested these hypotheses with syntenic inferences Bayesian models duplicate gene gain loss. Results predicted number (~170) based on current taxon sampling largely similar methods, but varies precise placement phylogeny. ‐based often yield alternative placements due variation substitution rates among lineages. Phylogenetic loss are more robust topological variation. However, errors can still produce spurious hypotheses, regardless method used. Conclusions showed agree average 3.5 individual species. phylogeny subject tree topology. As researchers continue test regarding impacts have evolution, it important consider as well methods.

Language: Английский

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Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Published: May 27, 2024

Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking step-change in the generation of data phylogenetic inference. While this advancement facilitated resolution many relationships, conflict continues to be reported, often attributed genome duplication, reticulation, deep coalescence or rapid speciation – processes that are particularly common evolution. The proliferation methods designed analyse target presence these can overwhelming researchers, especially students. In review, we guide researchers through bioinformatic workflow, with particular focus on robust inference conflict. Through highlight key considerations reducing artefactual conflict, synthesise strategies managing paralogs, explain causes measurement summarise current investigating biological underlying draw from examples Australian flora, review is broadly relevant any researcher working data. We conclude inherent inevitable but when properly managed, provide unprecedented insight into extraordinary complex histories plants.

Language: Английский

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A chromosome-level genome assembly of the varied leaved jewelflower, Streptanthus diversifolius, reveals a recent whole genome duplication

G3 Genes Genomes Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: March 18, 2025

Abstract The Streptanthoid complex, a clade of primarily Streptanthus and Caulanthus species in the Thelypodieae (Brassicaceae) is an emerging model system for ecological evolutionary studies. This complex spans full range California Floristic Province including desert, foothill, mountain environments. ability these related to radiate into dramatically different environments makes them desirable study subject exploring how plant expand their ranges adapt new over time. Ecological studies this have revealed fascinating variation serpentine soil adaptation, defense compounds, germination, flowering, life history strategies. Until now lack publicly available genome assemblies has hindered relate phenotypic observations underlying genetic molecular mechanisms. To help remedy situation, we present here chromosome-level assembly annotation diversifolius, member Complex, developed using Illumina, Hi-C, HiFi sequencing technologies. Construction also provides further evidence support previously reported recent whole duplication unique Thelypodieae. may provided individuals Complex arsenal rapidly throughout occupy commonly inhospitable soils.

Language: Английский

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Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome

Plants, Journal Year: 2025, Volume and Issue: 14(8), P. 1160 - 1160

Published: April 8, 2025

Transposon is the main component of eukaryotic genome, and more plant genome data show that transposons are diverse in regulating structure, variation, function evolution, with different transposition mechanisms genome. Hybridization polyploidy play an important role promoting speciation recent studies have shown usually accompanied by expansion transposons, which affect size structure polyploid plants. Transposons can insert into genes intergenic regions, resulting great differences overall closely related species, it also capture gene segments to increase copy number genes. In addition, influence epigenetic modification state regulate expression gene, while phenotype, biological abiotic stress response regulated transposons. Overall, especially adaptation evolution.

Language: Английский

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Ancient large‐scale gene duplications and diversification in bryophytes illuminate the plant terrestrialization

New Phytologist, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 24, 2024

Summary Large‐scale gene duplications (LSGDs) are crucial for evolutionary adaptation and recurrent in vascular plants. However, the role of ancient LSGDs terrestrialization diversification bryophytes, second most species‐rich group land plants, remains largely elusive due to limited sampling bryophytes. Employing extensive nuclear dataset bryophytes date, we reconstructed a time‐calibrated phylogenetic tree from 209 species, covering virtually all key bryophyte lineages, phylogenomic analyses diversification. We newly identified two LSGDs: one recent common ancestor (MRCA) extant another MRCA majority Jungermanniales s. lato . Duplicated genes these show significant enrichment photosynthesis‐related processes structures. Rhizoid‐responsive ROOTHAIR DEFECTIVE SIX‐LIKE ( RSL ) present rhizoidless challenging assumptions about rhizoid absence mechanisms. highlighted four major rate upshifts, which slightly postdated LSGDs, potentially linked flourishing gymnosperms angiosperms explaining over 80% diversity. Our findings, supported by sampling, highlight significance early offering new insights into plant evolution.

Language: Английский

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Species Tree Topology Impacts the Inference of Ancient Whole-Genome Duplications Across the Angiosperm Phylogeny

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 4, 2024

ABSTRACT Premise The history of angiosperms is marked by repeated rounds ancient whole-genome duplications (WGDs). Here we use state the art methods to provide an up-to-date view distribution WGDs in that considers both uncertainty introduced inference and alternative phylogenetic hypotheses. Methods Transcriptomic genomic data were used infer place across two hypothesized angiosperm phylogenies. Initial WGD hypotheses made using rate corrections synonymous divergences (K s ) paralogs orthologs. tested syntenic inferences Bayesian models duplicate gene gain loss phylogeny. Key results number (∼170) largely similar different methods, but there often variation precise placement on K based yield placements due substitution rates among lineages. Phylogenetic are more robust topological variation, allowing for post hoc testing However, errors species tree can still produce spurious regardless method used. Conclusions show agree average 3.5 species. phylogeny subject topology. As researchers continue test regarding impacts have evolution, it important consider as well methods.

Language: Английский

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doubletrouble:an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 29, 2024

Abstract Gene and genome duplications are major evolutionary forces that shape the diversity complexity of life. However, different duplication modes have distinct impacts on gene function, expression, regulation. Existing tools for identifying classifying duplicated genes either outdated or not user-friendly. Here, we present doubletrouble , an R/Bioconductor package provides a comprehensive robust framework analyzing from genomic data. can detect classify pairs as derived six (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, dispersed duplications), calculate substitution rates, signatures putative whole-genome events, visualize results publication-ready figures. We applied to repertoire in 822 eukaryotic genomes, which made available through user-friendly web interface (available at https://almeidasilvaf.github.io/doubletroubledb ). is freely accessible Bioconductor ( https://bioconductor.org/packages/doubletrouble ), it valuable resource study consequences duplications.

Language: Английский

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The genomes of Australian wild limes

Plant Molecular Biology, Journal Year: 2024, Volume and Issue: 114(5)

Published: Sept. 24, 2024

Abstract Australian wild limes occur in highly diverse range of environments and are a unique genetic resource within the genus Citrus . Here we compare haplotype-resolved genome assemblies six native limes, including four new generated using PacBio HiFi Hi-C sequencing data. The size genomes was between 315 391 Mb with contig N50s from 29.5 to 35 Mb. Gene completeness estimated be 98.4 99.3% annotations 97.7 98.9% based upon BUSCO, confirming high contiguity assembled genomes. High collinearity observed among two haplotype for each species. duplication evolutionary analysis demonstrated that citrus have undergone only one ancient whole-genome triplication event during evolution. highest number species-specific expanded gene families were found C. glauca they primarily enriched purine, thiamine metabolism, amino acids aromatic metabolism which might help mitigate drought, salinity, pathogen attacks drier this species is found. Unique genes related terpene biosynthesis, glutathione toll-like receptors australasica , starch sucrose both australis important candidate HLB tolerance these Expanded not lineage specific, however, greater plant-pathogen interactions, predominantly disease resistant protein,

Language: Английский

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Genomes of Poaceae sisters reveal key metabolic innovations preceding the emergence of grasses

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 7, 2024

SUMMARY The grass family (Poaceae, Poales) holds immense economic and ecological significance, exhibiting unique metabolic traits, including dual starch lignin biosynthetic pathways. To investigate when how the innovations known in grasses evolved, we sequenced genomes of a non-core grass, Pharus latifolius , non-grass graminids, Joinvillea ascendens Ecdeiocolea monostachya representing sister clade to Poaceae, Typha latifolia remaining Poales. rho whole genome duplication (ρWGD) ancestral lineage for all contributed gene expansions underlying cytosolic biosynthesis, whereas an earlier tandem phenylalanine ammonia lyase ( PAL ) gave rise phenylalanine/tyrosine PTAL responsible biosynthesis. Two mutations were sufficient expand function into PTAL. integrated genomic biochemical analyses relatives Poales revealed evolutionary molecular basis key grasses. Abstract Figure

Language: Английский

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Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants

in silico Plants, Journal Year: 2024, Volume and Issue: 6(2)

Published: Jan. 1, 2024

Abstract Gene regulatory networks (GRNs) based on transcription factors (TFs) control development and environmental responses. In this study, GRNs were inferred computationally using random forest decision tree-based regression. Networks constructed for the grasses barley, maize, wheat, brachypodium, sorghum rice. When compared with Arabidopsis thaliana alga networks, they show substantial conservation. The degree of conservation depends phylogenetic closeness. processes are conserved between all species include basic cellular functions while only in annotated more specific gene ontology terms. three a carbon concentration mechanism, photorespiration is partially dissociated from photosynthetic regulation. contrast, C4 species, regulation genes associated comparative analyses reveal TFs that photosynthesis seed plants but not alga. resulted pipeline general transfer information small dicot A. commercially relevant grasses.

Language: Английский

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