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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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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Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(21)

Published: May 17, 2021

Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number studies have demonstrated genomic parallelism, yet magnitude this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that scales with genetic divergence between lineages, but is case and underlying processes remain unknown. Here, we resequenced seven parallel lineages two

Language: Английский

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Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Dec. 20, 2019

Abstract Polyploidization is frequently associated with increased transposable element (TE) content. However, what drives TE dynamics following whole genome duplication (WGD) and the evolutionary implications remain unclear. Here, we leverage whole-genome resequencing data available for ~300 individuals of Arabidopsis arenosa , a well characterized natural diploid-autotetraploid plant species, to address these questions. Based on 43,176 insertions detect in genomes, demonstrate that relaxed purifying selection rather than transposition bursts main driver over-accumulation after WGD. Furthermore, pool tetraploids especially enriched within or near environmentally responsive genes. Notably, show major flowering-time repressor gene FLC disrupted by insertion specifically rapid-cycling tetraploid lineage colonized mainland railways. Together, our findings indicate tetrasomy leads an enhanced accumulation genic insertions, some which likely contribute local adaptation.

Language: Английский

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Structure is more robust than other clustering methods in simulated mixed-ploidy populations

Heredity, Journal Year: 2019, Volume and Issue: 123(4), P. 429 - 441

Published: July 8, 2019

Analysis of population genetic structure has become a standard approach in genetics. In polyploid complexes, clustering analyses can elucidate the origin populations and patterns admixture between different cytotypes. However, combining diploid data theoretically lead to biased inference with (artefactual) by ploidy. We used simulated mixed-ploidy (diploid-autotetraploid) systematically compare performance k-means model-based methods implemented Structure, Admixture, FastStructure InStruct under scenarios differentiation marker types. Under strong differentiation, tested applications performed equally well. when was weak, Structure only method that allowed unbiased markers limited genotypic information (co-dominant unknown dosage or dominant markers). Still, since comparatively slow, much faster but less powerful provides reasonable alternative for large datasets. Finally, although bias makes unsuitable incomplete genotype information, numbers loci (>1000) known superior terms power speed. conclude is most robust analysis populations, should be considered some specific conditions.

Language: Английский

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Interspecific introgression mediates adaptation to whole genome duplication

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Nov. 18, 2019

Abstract Adaptive gene flow is a consequential phenomenon across all kingdoms. Although recognition increasing, there no study showing that bidirectional mediates adaptation at loci manage core processes. We previously discovered concerted molecular changes among interacting members of the meiotic machinery controlling crossover number upon to whole-genome duplication (WGD) in Arabidopsis arenosa . Here we conduct population genomic test hypothesis WGD has been mediated by adaptive between A. and lyrata find underwent more recently than , suggesting pre-adapted alleles have rescued nascent but also detect opposite direction functionally under most extreme levels selection. These data indicate allowed for survival after WGD, merger these species greater sum their parts.

Language: Английский

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Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa

Proceedings of the National Academy of Sciences, Journal Year: 2020, Volume and Issue: 117(16), P. 8980 - 8988

Published: April 9, 2020

Polyploidy, which results from whole genome duplication (WGD), has shaped the long-term evolution of eukaryotic genomes in all kingdoms. Polyploidy is also implicated adaptation, domestication, and speciation. Yet when WGD newly occurs, resulting neopolyploids face numerous challenges. A particularly pernicious problem segregation multiple chromosome copies meiosis. Evolution can overcome this challenge, likely through modification pairing recombination to prevent deleterious multivalent associations, but molecular basis remains mysterious. We study mechanisms underlying evolutionary stabilization polyploid meiosis using Arabidopsis arenosa, a relative A. thaliana with natural diploid meiotically stable autotetraploid populations. Here we investigate effects ancestral (diploid) versus derived (tetraploid) alleles two genes, ASY1 ASY3, that were among several genes under selection tetraploid lineage. These encode interacting proteins critical for formation meiotic axes, long linear multiprotein structures form along sister chromatids are essential recombination, segregation, fertility. show both associated changes meiosis, including reduced multichromosome axis length, tendency more rod-shaped bivalents metaphase I. Thus, conclude ASY3 components larger multigenic solution individual have subtle effects. Our relevant understanding generally how traits evolve faced

Language: Английский

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Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(5), P. 1434 - 1451

Published: Jan. 23, 2021

Abstract Non‐random mating among individuals can lead to spatial clustering of genetically similar and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, have parentage single populations or involving hybridization between differentiated Accounting for this mixture structure important when mapping the genetics traits learning about formative evolutionary processes that shape genetic variation Stratified relatedness quantified using estimates ancestry are derived a statistical model. Development these models polyploid mixed‐ploidy has lagged behind those diploids. Here, we extend test hierarchical Bayesian model, called entropy , which use low‐depth sequence data estimate genotype parameters autopolyploid (including sex chromosomes autosomes within individuals). Our analysis simulated illustrated trade‐off sequencing depth genome coverage found lower error associated with across larger fraction than high‐depth smaller genome. The model high accuracy sensitivity as verified through admixture diploid tetraploid Arabidopsis arenosa .

Language: Английский

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Defective pollen tube tip growth induces neo-polyploid infertility

Science, Journal Year: 2024, Volume and Issue: 383(6686)

Published: Feb. 29, 2024

Genome duplication (generating polyploids) is an engine of novelty in eukaryotic evolution and a promising crop improvement tool. Yet newly formed polyploids often have low fertility. Here we report that severe fertility-compromising defect pollen tube tip growth arises new

Language: Английский

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