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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SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome‐specific k‐mers

New Phytologist, Journal Year: 2022, Volume and Issue: 235(2), P. 801 - 809

Published: April 23, 2022

Summary With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome‐phasing algorithm, S ub P haser , specifically designed neoallopolyploid homoploid hybrid. first searches subgenome‐specific sequence ( k ‐mer), then assigns homoeologous chromosomes into subgenomes, further provides tools annotate investigate specific sequences. works well on neoallopolyploids hybrids containing sequences like wheat, but fails autopolyploids lacking alfalfa, indicating that can phase neoallopolyploid/homoploid with high accuracy, sensitivity performance. This highly accurate, sensitive, ancestral data free chromosome phasing offers significant application value subgenome in hybrids, subsequent exploration related genetic/epigenetic mechanisms.

Language: Английский

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Impact of polyploidy on plant tolerance to abiotic and biotic stresses

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Aug. 22, 2022

Polyploidy, defined as the coexistence of three or more complete sets chromosomes in an organism's cells, is considered a pivotal moving force evolutionary history vascular plants and has played major role domestication several crops. In last decades, improved cultivars economically important species have been developed artificially by inducing autopolyploidy with chemical agents. Studies on diverse shown that anatomical physiological changes generated either natural artificial polyploidization can increase tolerance to abiotic biotic stresses well disease resistance, which may positively impact plant growth net production. The aim this work review current literature regarding link between ploidy level stressors, emphasis molecular mechanisms responsible for these effects, their development both polyploids, during exposure adverse environmental conditions. We focused analysis those types stressors progress made knowledge putative morpho-physiological and/or involved, revealing factors common, need be addressed future research.

Language: Английский

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Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 22, 2024

Abstract Whole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms. However, empirical evidence for rediploidization, major process where polyploids give rise to diploid descendants, is still lacking at genomic level. Here we present chromosome-scale genomes mangrove tree Sonneratia alba related inland plant Lagerstroemia speciosa . Their common ancestor has experienced a whole-genome triplication (WGT) approximately 64 million years ago coinciding with period dramatic global climate change. , adapting habitats, extensive chromosome rearrangements post-WGT. We observe WGT retentions display sequence expression divergence, suggesting potential neo- sub-functionalization. Strong selection acting on three-copy indicates adaptive value response new environments. To elucidate role ploidy changes genome evolution, improve model polyploidization–rediploidization based evidence, contributing understanding evolution during

Language: Английский

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Genomics of Evolutionary Novelty in Hybrids and Polyploids

Frontiers in Genetics, Journal Year: 2020, Volume and Issue: 11

Published: July 28, 2020

It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically as significant speciation adaptation, recognition of the importance interspecific gene flow dramatically increased during genomics era, concomitant with an unending flood empirical examples, or without genome doubling. Interspecific is thus increasingly thought to lead evolutionary innovation diversification, via adaptive introgression, homoploid hybrid allopolyploid speciation. Less well understood, however, suite genetic genomic mechanisms set motion by merger differentiated genomes, temporal scale over which recombinational complexity mediated might be expressed exposed natural selection. We focus on these issues here, considering types molecular saltational event between two diverged species, either doubling, how various can contribute novel phenotypes. Genetic include infusion new alleles genesis structural variation including translocations inversions, homoeologous exchanges, transposable element mobilization insertional effects, presence-absence copy number variation. Polyploidy generates massive transcriptomic regulatory alteration, presumably disrupted stoichiometries factors, small RNAs other interactions cascade from single-gene expression change up through entire networks transformed modules. highlight both combinatorial possibilities range scales such generated, selection drift.

Language: Английский

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The Scaling of Genome Size and Cell Size Limits Maximum Rates of Photosynthesis with Implications for Ecological Strategies

International Journal of Plant Sciences, Journal Year: 2019, Volume and Issue: 181(1), P. 75 - 87

Published: Sept. 30, 2019

A central challenge in plant ecology is to define the major axes of functional variation with direct consequences for fitness. Central three main components fitness (growth, survival, and reproduction) rate metabolic conversion CO2 into carbon that can be allocated various structures functions. Here we (1) argue a primary constraint on maximum photosynthesis per unit leaf area size packing density cells (2) show genome strong predictor cell sizes, densities, across terrestrial vascular plants. Regardless genic content associated size, simple biophysical constraints encapsulating lower limit upper as well range possible sizes densities. Genome therefore, acts first-order gain predicted limits allocation growth, reproduction, defense. The effects metabolism, have broad implications biogeography other theories suggest selection metabolism may role evolution.

Language: Английский

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Repeat-sequence turnover shifts fundamentally in species with large genomes

Nature Plants, Journal Year: 2020, Volume and Issue: 6(11), P. 1325 - 1329

Published: Oct. 19, 2020

Language: Английский

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When everything changes at once: finding a new normal after genome duplication

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2020, Volume and Issue: 287(1939), P. 20202154 - 20202154

Published: Nov. 18, 2020

Whole-genome duplication (WGD), which leads to polyploidy, is implicated in adaptation and speciation. But what are the immediate effects of WGD how do newly polyploid lineages adapt them? With many studies new evolved polyploids now available, along with genes under selection polyploids, we an increasingly good position understand polyploidy generates novelty. Here, I will review consistent on biology plants, such as increase cell size, increased stress tolerance more. discuss a change something fundamental size can challenge function some types particular. also have learned about short- medium-term evolutionary response WGD. It clear that this may ‘lock in’ traits happen be beneficial, while other cases, it might more ‘emergency response’ work around physiological changes either deleterious, or cannot undone context. Yet, return rapidly diploid-like state. Polyploids may, by re-jigging inter-related processes, find new, conditionally adaptive, normal.

Language: Английский

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Epigenetics and the success of invasive plants

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2021, Volume and Issue: 376(1826), P. 20200117 - 20200117

Published: April 17, 2021

Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the evolutionary processes that underly invasion success in order successfully manage existing invaders, prevent future invasions. As successful invasive species sometimes are suspected rapidly adjust their new environments spite of very low genetic diversity, we obliged re-evaluate genomic-level translate into phenotypic diversity. In this paper, review work supports idea trait variation, within among populations, can be created through epigenetic or other non-genetic processes, particularly clonal invaders where somatic changes persist indefinitely. We consider several have been implicated as adaptive success, focusing various forms 'genomic shock' resulting from exposure environmental stress, hybridization whole-genome duplication (polyploidy), leading patterns gene expression re-programming contribute variation even novelty. These mechanisms transgressive phenotypes, including hybrid vigour novel traits, may thus help huge successes some plant especially those genetically impoverished. This article part theme issue 'How does epigenetics influence course evolution?'

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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