Polyploidy: an evolutionary and ecological force in stressful times

The Plant Cell, Journal Year: 2020, Volume and Issue: 33(1), P. 11 - 26

Published: Dec. 1, 2020

Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for innovation species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests link with environmental conditions. Whole-genome seem correlate periods extinction or global change, while polyploids often thrive in harsh disturbed environments. Evidence is also accumulating that biotic interactions, instance, pathogens mutualists, affect differently than nonpolyploids. Here, we review recent findings insights on effect abiotic stress versus nonpolyploids propose response general important even determining factor success polyploidy.

Language: Английский

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Giant lungfish genome elucidates the conquest of land by vertebrates

Nature, Journal Year: 2021, Volume and Issue: 590(7845), P. 284 - 289

Published: Jan. 18, 2021

Abstract Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, ‘conquered’ land and ultimately gave rise all vertebrates, including humans 1–3 . Here we determine chromosome-quality genome of Australian lungfish ( Neoceratodus forsteri ), which is known have largest any animal. The vast size this genome, about 14× larger than that humans, attributable mostly huge intergenic regions introns with high repeat content (around 90%), components resemble those tetrapods (comprising mainly long interspersed nuclear elements) more they do ray-finned fish. continues expand independently (its transposable elements are still active), through mechanisms different enormous genomes salamanders. 17 fully assembled macrochromosomes maintain synteny other vertebrate chromosomes, microchromosomes conserved ancient homology ancestral karyotype. Our phylogenomic analyses confirm previous reports occupy a key evolutionary position as closest living relatives 4,5 , underscoring importance for understanding innovations associated terrestrialization. Lungfish preadaptations on include gain limb-like expression developmental genes such hoxc13 sall1 their lobed fins. Increased rates evolution duplication obligate air-breathing, lung surfactants expansion odorant receptor gene families (which encode proteins involved detecting airborne odours), contribute tetrapod-like biology lungfishes. These findings advance our major transition during evolution.

Language: Английский

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Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: April 4, 2023

Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs transcriptome, critical for determining traits that influence wheat growth and development. Asymmetric transcription has been so far investigated in a tissue or organ-specific manner, which could be misleading due mixture cell types.

Language: Английский

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Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(4), P. 812 - 828

Published: Jan. 17, 2024

Abstract Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these are gaining traction in molecular developmental biology for elucidating transcriptional changes across cell types a specific tissue or organ, upon treatments, response to biotic abiotic stresses, between genotypes. Despite rapidly accelerating use technologies, collective standardized experimental analytical procedures support acquisition high-quality data sets still missing. In this commentary, we discuss common challenges associated with single-cell transcriptomics plants propose general guidelines improve reproducibility, quality, comparability, interpretation make readily available community fast-developing field research.

Language: Английский

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Polyploid phylogenetics

New Phytologist, Journal Year: 2021, Volume and Issue: 230(1), P. 66 - 72

Published: Jan. 25, 2021

Summary Polyploidy is a dominant feature of extant plant diversity. However, major research questions, including whether polyploidy important to long‐term evolution or just ‘evolutionary noise’, remain unresolved due difficulties associated with the generation and analysis data from polyploid lineages. Many these have been recently overcome, such that it now often relatively straightforward infer full reticulate phylogenetic history groups formed polyploids. This nascent field ‘polyploid phylogenetics’ allows researchers tackle long‐standing questions macroevolution, supplies foundation for mechanistic models ploidy change, provides opportunity include more complete representative sample taxa in our analyses general.

Language: Английский

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Genome downsizing after polyploidy: mechanisms, rates and selection pressures

The Plant Journal, Journal Year: 2021, Volume and Issue: 107(4), P. 1003 - 1015

Published: June 2, 2021

SUMMARY An analysis of over 10 000 plant genome sizes (GSs) indicates that most species have smaller genomes than expected given the incidence polyploidy in their ancestries, suggesting selection for downsizing. However, comparing ancestral GS with suggests rate DNA loss following is likely to been very low (4–70 Mb/million years, 4–482 bp/generation). This poses a problem. How might such small losses be visible selection, overcome power genetic drift and drive downsizing? Here we explore problem, focussing on role double‐strand break (DSB) repair pathways (non‐homologous end joining homologous recombination) may played. We also two hypotheses could explain how favour downsizing polyploidy: reduce (i) nitrogen (N) phosphate (P) costs associated nucleic acid synthesis nucleus transcriptome (ii) impact scaling effects cell size, which influences CO 2 uptake water loss. hypothesis must fastest early polyploid generations. Alternatively, if more continuous process evolutionary time, then propose it byproduct elsewhere, as limiting damaging activity repetitive DNA. If so, photosynthesis, use efficiency and/or nutrient at level emergent properties, advantages, but not ones selected generational timescales.

Language: Английский

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Cancer recurrence and lethality are enabled by enhanced survival and reversible cell cycle arrest of polyaneuploid cells

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(7)

Published: Jan. 27, 2021

We present a unifying theory to explain cancer recurrence, therapeutic resistance, and lethality. The basis of this is the formation simultaneously polyploid aneuploid cells, polyaneuploid cells (PACCs), that avoid toxic effects systemic therapy by entering state cell cycle arrest. independent which classically associated oncogenic mutations have already occurred. PACCs been generally disregarded as senescent or dying cells. Our states resistance driven PACC enabled accessing program allows an double its genomic content, followed entry into nondividing protect DNA integrity ensure survival. Upon removal stress, e.g., chemotherapy, undergo depolyploidization generate resistant progeny make up bulk within tumor.

Language: Английский

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Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome

Nature Plants, Journal Year: 2021, Volume and Issue: 7(9), P. 1239 - 1253

Published: Sept. 2, 2021

Abstract Aristolochia , a genus in the magnoliid order Piperales, has been famous for centuries its highly specialized flowers and wide medicinal applications. Here, we present new, high-quality genome sequence of fimbriata species that, similar to Amborella trichopoda lacks further whole-genome duplications since origin extant angiosperms. As such, A. is an excellent reference inferences angiosperm evolution, enabling detection two novel Piperales dating previously reported other magnoliids. Genomic comparisons between angiosperms facilitated identification ancient genomic rearrangements suggesting placement magnoliids as sister monocots, whereas phylogenetic based on data compiled yielded ambiguous relationships. By identifying associated homologues investigating their evolutionary histories expression patterns, revealed conserved floral developmental genes distinct downstream regulatory network that may contribute complex flower morphology . Finally, elucidated genetic basis underlying biosynthesis terpenoids aristolochic acids

Language: Английский

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Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: April 7, 2022

All extant core-eudicot plants share a common ancestral genome that has experienced cyclic polyploidizations and (re)diploidizations. Reshuffling of the generates abundant genomic diversity, but role this diversity in shaping hierarchical architecture, such as chromatin topology gene expression, remains poorly understood. Here, we assemble chromosome-level genomes one diploid three tetraploid Panax species conduct in-depth comparative epigenomic analyses. We show chromosomal interactions within each duplicated chromosome largely maintain species, albeit experiencing ca. 100-150 million years evolution from shared ancestor. Biased genetic fractionation epigenetic regulation divergence during polyploidization/(re)diploidization processes generate remarkable biochemical secondary metabolites genus. Our study provides paleo-polyploidization perspective how reshuffling leads to highly dynamic metabolic diversification eudicot plants.

Language: Английский

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Polyploidy as a Fundamental Phenomenon in Evolution, Development, Adaptation and Diseases

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(7), P. 3542 - 3542

Published: March 24, 2022

DNA replication during cell proliferation is ‘vertical’ copying, which reproduces an initial amount of genetic information. Polyploidy, results from whole-genome duplication, a fundamental complement to vertical copying. Both organismal and polyploidy can emerge via premature cycle exit or cell-cell fusion, the latter giving rise polyploid hybrid organisms epigenetic hybrids somatic cells. Polyploidy-related increase in biological plasticity, adaptation, stress resistance manifests evolution, development, regeneration, aging, oncogenesis, cardiovascular diseases. Despite prevalence nature importance for medicine, agri- aquaculture, processes mechanisms underlying these features largely remain unknown. The evolutionarily conserved include activation transcription, response stress, damage hypoxia, induction programs morphogenesis, unicellularity, longevity, suggesting that common confer adaptive viability, cells organisms. By increasing polyploidization provide survival under stressful conditions where diploid cannot survive. However, it occurs at expense specific function, thus promoting developmental programming adult diseases risk cancer. Notably, genes arising evolutionary are heavily involved cancer other Ploidy-related changes gene expression presumably originate chromatin modifications derepression bivalent genes. provided evidence elucidates role carcinogenesis, may contribute development new strategies regeneration preventing

Language: Английский

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