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104 results for “allopolyploid”
Data from: Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
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Data from: Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors
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Data from: Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica
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Data from: A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features
The origin and evolution of polyploids have been studied extensively in angiosperms and ferns but very rarely in gymnosperms. With the exception of three species of conifers, all natural polyploid species of gymnosperms belong to Ephedra, in which more than half of the species show polyploid cytotypes. Here we investigate the origin and evolution of polyploids of Ephedra distributed in the Qinghai-Tibetan Plateau (QTP) and neighboring areas. Flow cytometry (FCM) was used to measure the ploidy levels of the sampled species that are represented by multiple individuals from different populations, and then two single-copy nuclear genes (LFY and DDB2) and two chloroplast DNA fragments were used to unravel the possible origins and maternal donors of the polyploids. The results indicate that the studied polyploid species are allopolyploids, and suggest that allotetraploidy is a dominant mode of speciation in Ephedra. The high percentage of polyploids in the genus could be related to some of its biological attributes such as vegetative propagation, a relatively high rate of unreduced gamete formation, and a small genome size relative to most other gymnosperms. Significant ecological divergences between allotetraploids and their putative progenitors were detected by PCA analyses and ANOVA and Tukey's tests, with the exception of E. saxatilis. The overlap of geographical distributions and ecological niches of some diploid species could have provided opportunities for interspecific hybridization and allopolyploid speciation.
Data from: Morphological convergence between an allopolyploid and one of its parental species correlates with biased gene expression and DNA loss
The contribution of gene expression modulation to phenotypic evolution is of major importance to an understanding of the origin of divergent or convergent phenotypes during and following polyploid speciation. Here we analysed genome-wide gene expression in two subspecies of the allotetraploid species, Senecio mohavensis A. Gray, and its diploid parents S. flavus (Decne.) Sch. Bip. and S. glaucus L.. The tetraploid is morphologically much more similar to S. flavus, leading to earlier confusion over its taxonomic status. By means of an analysis of transcriptomes of all three species, we show that gene expression divergence between the parent species is relatively low (ca. 14% of loci), whereas there is significant unequal expression between ca. 20-25% of the parental homoeologues (gene copies) in the tetraploid. The majority of the expression bias in the tetraploid is in favour of S. flavus homoeologues (ca. 65% of the differentially expressed loci), and overall expression of this parental species sub-genome is higher than that of the S. glaucus sub-genome. To determine whether absence of expression of a particular S. glaucus homoeologue in the allotetraploid could be due to loss of DNA, we carried out a PCR-based assay and confirmed that in three out of 10 loci the S. glaucus homoeologue appeared absent. Our results suggest that biased gene expression is one cause of the allotetraploid S. mohavensis being more similar in morphology to one of its parent, S. flavus, and that such bias could result, in part, from loss of S. glaucus homoeologues at some loci in the allotetraploid.
Data from: Assignment of homoeologues to parental genomes in allopolyploids for species tree inference, with an example from Fumaria (Papaveraceae)
There is a rising awareness that species trees are best inferred from multiple loci while taking into account processes affecting individual gene trees, such as substitution model error (failure of the model to account for the complexity of the data) and coalescent stochasticity (presence of incomplete lineage sorting). Although most studies have been carried out in the context of dichotomous species trees, these processes operate also in more complex evolutionary histories involving multiple hybridizations and polyploidy. Recently, methods have been developed that accurately handle incomplete lineage sorting in allopolyploids, but they are thus far restricted to networks of diploids and tetraploids. We propose a procedure that improves on this limitation by designing a workflow that assigns homoeologues to hypothetical diploid ancestral genomes prior to genome tree construction. Conflicting assignment hypotheses are evaluated against substitution model error and coalescent stochasticity. Incongruence that cannot be explained by stochastic mechanisms needs to be explained by other processes (e.g., homoploid hybridization or paralogy). The data can then be filtered to build multilabeled genome phylogenies using inference methods that can recover species trees, either in the face of substitution model error and coalescent stochasticity alone, or while simultaneously accounting for hybridization. Methods are already available for folding the resulting multilabeled genome phylogeny into a network. We apply the workflow to the reconstruction of the reticulate phylogeny of the plant genus Fumaria (Papaveraceae) with ploidal levels ranging from 2x to 14x. We describe the challenges in recovering nuclear NRPB2 homoeologues in high ploidy species while combining in vivo cloning and direct sequencing techniques. Using parametric bootstrapping simulations we assign nuclear homoeologues and chloroplast sequences (four concatenated loci) to their common hypothetical diploid ancestral genomes. As these assignments hinge on effective population size assumptions, we investigate how varying these assumptions impacts the recovered multilabeled genome phylogeny.
Data from: Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus)
Whole genome duplication (WGD), the doubling of the nuclear DNA of a species, contributes to biological innovation by creating genetic redundancy. One mode of WGD is allopolyploidization, wherein each genome from two ancestral species becomes a 'subgenom' of a polyploid descendant species. The evolutionary trajectory of a duplicated gene that arises from WGD is influenced both by natural selection, creating new or partitioning functions, and by gene silencing (pseudogenization). Here, we explored how these two phenomena varied over time and within allopolyploid genomes in several allotetraploid clawed frog species (Xenopus). Our analysis demonstrates that, across these polyploid genomes, purifying selection was greatly relaxed compared to a diploid outgroup, was asymmetric between each subgenome, and that coding regions are shorter in the subgenome with more relaxed purifying selection. As well, we found that the rate of gene loss was higher in the subgenome under weaker purifying selection and has remained relatively consistent over time after WGD. Our findings provide perspective from vertebrates on the evolutionary forces that likely shape allopolyploid genomes on other branches of the tree of life.
Figure 3 from: Vallejo-Marin M (2012) Mimulus peregrinus (Phrymaceae): A new British allopolyploid species. PhytoKeys 14: 1-14. https://doi.org/10.3897/phytokeys.14.3305
Figure 3 - Flow-cytometry estimates of 2C DNA content (DAPI-stained) of British Mimulus. Error bars represent standard errors when multiple individuals per taxon were tested. Sample sizes as follows (chromosome numbers for each population are given in parenthesis when available). Mimulus guttatus: N = 4 individuals from Dunblane, Perthshire (2n = 28); and 2 individuals from Muckle Roe, Shetland; Mimulus × robertsii (= Mimulus guttatus × Mimulus luteus): N= 1 individual from Nenthall, Cumbria (2n = 44, 45); Mimulus × smithii (= Mimulus luteus var. luteus × Mimulus luteus var. variegatus): N = 2 individuals from Coldstream, Scottish Borders (2n = 59, 60, 61, 62); Mimulus peregrinus: N = 6 individuals from Leadhills, South Lanarkshire (2n = 92).All chromosome counts kindly provided by J. Bailey.
Figure 2 from: Vallejo-Marin M (2012) Mimulus peregrinus (Phrymaceae): A new British allopolyploid species. PhytoKeys 14: 1-14. https://doi.org/10.3897/phytokeys.14.3305
Figure 2 - Flowers of Mimulus peregrinus and closely related taxa. A Mimulus guttatus B Mimulus × smithii (Mimulus luteus luteus × Mimulus luteus variegatus) C Mimulus × robertsii (Mimulus guttatus × Mimulus luteus), and D Mimulus peregrinus. Each taxon is represented by flowers from two individuals from a single locality to illustrate within-population variability: Mimulus guttatus = Dunblane, Perthshire; Mimulus × smithii = Coldstream, Scottish Borders; Mimulus × robertsii = Nenthall, Cumbria; Mimulus peregrinus = Leadhills, South Lanarkshire. Scale bar = 1cm.
Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica
<p>Plant cells arose through the endosymbiotic engulfment of a cyanobacterium that subsequently formed the chloroplast genome, enabling plants to develop new critical functions. Almost all chloroplast proteins are now encoded in the nucleus, but some chloroplast protein complexes are jointly encoded by both nuclear and chloroplast genes, which interact to facilitate essential plant functions, such as the photosystems. Allopolyploidy, resulting from the hybridization and genome doubling of two divergent species, can disrupt these fine-tuned cytonuclear interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparental organelle inheritance. Such unequal genome inheritance may affect the conformation of the five cytonuclear complexes in allopolyploids. We used <em>Brassica</em> as a model to study the effects of paleopolyploidy and dichotomic divergence in parental species, as well as the effects of recent allopolyploidy in <em>Brassica napus</em>, on genes implicated in cytonuclear complexes. Because the <em>B. napus</em> parental diploid species are paleohexaploids, we first identified paleologous copies of cytonuclear complex genes. We found that these genes are preferentially retained in duplicates, are nearly all transcribed and are undergoing strong purifying selection, in accordance with the ‘gene balance hypothesis’. Subsequently, we compared expression patterns of cytonuclear complex homoeolog genes between resynthesized <em>B. napus </em>individuals and their respective diploid parents. The neo-polyploids showed neither biased sub-genome expression nor homogenization of homoeologs, due to highly conserved parental chloroplast genomes. These findings provide new insights and an innovative framework to understand the impact of cytonuclear interactions on interspecific hybridization and allopolyploid speciation.</p>
Fig. 3 in Flavonoid pattern inheritance in the allopolyploid Spartina anglica - Comparison with the parental species S. maritima and S. alterniflora
Fig. 3. Formulae of compounds 1–20.
Data from: Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus)
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Data from: Assignment of homoeologues to parental genomes in allopolyploids for species tree inference, with an example from Fumaria (Papaveraceae)
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Data from: Molecular data and ploidal levels indicate several putative allopolyploidization events in the genus Potentilla (Rosaceae)
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Data from: Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor
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Data from: Speciation by genome duplication: repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus
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Data from: A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features
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Data from: Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting
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Data from: Multi-speed genome diploidization and diversification after an ancient allopolyploidization
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Data from: Morphological convergence between an allopolyploid and one of its parental species correlates with biased gene expression and DNA loss
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