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Genome Research Feb 2022Genotyping from sequencing is the basis of emerging strategies in the molecular breeding of polyploid plants. However, compared with the situation for diploids, in which...
Genotyping from sequencing is the basis of emerging strategies in the molecular breeding of polyploid plants. However, compared with the situation for diploids, in which genotyping accuracies are confidently determined with comprehensive benchmarks, polyploids have been neglected; there are no benchmarks measuring genotyping error rates for small variants using real sequencing reads. We previously introduced a variant calling method, Octopus, that accurately calls germline variants in diploids and somatic mutations in tumors. Here, we evaluate Octopus and other popular tools on whole-genome tetraploid and hexaploid data sets created using in silico mixtures of diploid Genome in a Bottle (GIAB) samples. We find that genotyping errors are abundant for typical sequencing depths but that Octopus makes 25% fewer errors than other methods on average. We supplement our benchmarks with concordance analysis in real autotriploid banana data sets.
Topics: Benchmarking; Genotype; High-Throughput Nucleotide Sequencing; Humans; Polyploidy
PubMed: 34965940
DOI: 10.1101/gr.275579.121 -
Current Opinion in Plant Biology Apr 2018Polyploidy may provide adaptive advantages and is considered to be important for evolution and speciation. Polyploidy events are found throughout the evolutionary... (Review)
Review
Polyploidy may provide adaptive advantages and is considered to be important for evolution and speciation. Polyploidy events are found throughout the evolutionary history of plants, however they do not seem to be uniformly distributed along the time axis. For example, many of the detected ancient whole-genome duplications (WGDs) seem to cluster around the K/Pg boundary (∼66Mya), which corresponds to a drastic climate change event and a mass extinction. Here, we discuss more recent polyploidy events using Arabidopsis as the most developed plant model at the level of the entire genus. We review the history of the origin of allotetraploid species A. suecica and A. kamchatica, and tetraploid lineages of A. lyrata, A. arenosa and A. thaliana, and discuss potential adaptive advantages. Also, we highlight an association between recent glacial maxima and estimated times of origins of polyploidy in Arabidopsis. Such association might further support a link between polyploidy and environmental challenge, which has been observed now for different time-scales and for both ancient and recent polyploids.
Topics: Arabidopsis; Evolution, Molecular; Genetic Variation; Genome, Plant; Phylogeny; Polyploidy
PubMed: 29448159
DOI: 10.1016/j.pbi.2018.01.005 -
The New Phytologist Oct 2018Contents Summary 87 I. Introduction 87 II. Evolution in action: subgenome dominance within newly formed hybrids and polyploids 88 III. Summary and future directions 90... (Review)
Review
Contents Summary 87 I. Introduction 87 II. Evolution in action: subgenome dominance within newly formed hybrids and polyploids 88 III. Summary and future directions 90 Acknowledgements 92 References 92 SUMMARY: The merger of divergent genomes, via hybridization or allopolyploidization, frequently results in a 'genomic shock' that induces a series of rapid genetic and epigenetic modifications as a result of conflicts between parental genomes. This conflict among the subgenomes routinely leads one subgenome to become dominant over the other subgenome(s), resulting in subgenome biases in gene content and expression. Recent advances in methods to analyze hybrid and polyploid genomes with comparisons to extant parental progenitors have allowed for major strides in understanding the mechanistic basis for subgenome dominance. In particular, our understanding of the role that homoeologous exchange might play in subgenome dominance and genome evolution is quickly growing. Here we describe recent discoveries uncovering the underlying mechanisms and provide a framework to predict subgenome dominance in hybrids and allopolyploids with far-reaching implications for agricultural, ecological, and evolutionary research.
Topics: Epigenesis, Genetic; Evolution, Molecular; Gene Expression Regulation, Plant; Genome, Plant; Hybridization, Genetic; Polyploidy
PubMed: 29882360
DOI: 10.1111/nph.15256 -
Proceedings of the National Academy of... Nov 2022Whole genome duplications (WGDs) are one of the most dramatic mutations that can be found in nature. The effects of WGD vary dramatically but can have profound impacts...
Whole genome duplications (WGDs) are one of the most dramatic mutations that can be found in nature. The effects of WGD vary dramatically but can have profound impacts on an organism's expression, cytotype, and phenotype, altering their evolutionary trajectory as a result. Despite the growing appreciation for the contribution of WGDs in animal evolution, the significant factors influencing how polyploid animal lineages are established and maintained are still not well understood. Many hypotheses have been proposed which predict how climate and environment may influence polyploid incidence and evolution. To test and distinguish between these hypotheses, I assembled a global dataset of polyploid occurrences in three animal clades (Amphibia, Actinopterygii, and Insecta). The dataset encompasses chromosomal, phylogenetic, environmental, and climatic data across 57,905 species in 2,223 terrestrial, freshwater, and marine ecoregions. My analysis reveals a strong latitudinal gradient in all three clades, with the tendency for polyploid taxa to occur more frequently at higher latitudes. Many variables were significant (phylogenetic ANOVA < 0.05 after Bonferroni correction) between polyploids and diploids across taxa, notably those pertaining to temperature dynamics and glaciation. Glaciation in particular appears to be the most significant driver of polyploidy in animals, as these models had the highest relative likelihoods consistently across clades. These results contribute to a model of evolution wherein the broader genomic toolkit of polyploids facilitates adaptation and ecological resilience, enabling polyploids to colonize new or rapidly changing environments.
Topics: Animals; Phylogeny; Polyploidy; Diploidy; Insecta; Adaptation, Physiological
PubMed: 36409908
DOI: 10.1073/pnas.2214070119 -
The New Phytologist Feb 2015Genomic evidence of ancestral whole genome duplication (WGD) and polyploidy is widespread among eukaryotic species, and especially among plants. WGD is thought to... (Review)
Review
Genomic evidence of ancestral whole genome duplication (WGD) and polyploidy is widespread among eukaryotic species, and especially among plants. WGD is thought to provide the raw material for adaptation in the form of duplicated genes, and polyploids are thought to benefit from both physiological and genetic buffering. Comparatively little attention has focused on the genomic challenge of polyploidy, however, although much evidence exists that polyploidy severely perturbs important cellular functions. Here, I review recent progress in the study of the re-establishment of stable meiosis in recently evolved polyploids, focusing on four plant species. This work has yielded an insight into the mechanisms underlying stabilization of genome transmission in polyploids, and is revealing remarkable parallels among diverse taxa. Importantly, these studies also provide a road map for investigating how polyploids respond to the challenge of WGD.
Topics: Adaptation, Physiological; Biological Evolution; Environment; Gene Duplication; Genes, Plant; Genome, Plant; Meiosis; Plant Cells; Plants; Polyploidy
PubMed: 25729801
DOI: 10.1111/nph.12939 -
The Plant Cell Mar 2021Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms,... (Review)
Review
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
Topics: Biological Evolution; Evolution, Molecular; Genome, Plant; Polyploidy
PubMed: 33751096
DOI: 10.1093/plcell/koaa015 -
Genes Sep 2021Plant cytogenetic studies have provided essential knowledge on chromosome behavior during meiosis, contributing to our understanding of this complex process. In this... (Review)
Review
Plant cytogenetic studies have provided essential knowledge on chromosome behavior during meiosis, contributing to our understanding of this complex process. In this review, we describe in detail the meiotic process in auto- and allopolyploids from the onset of prophase I through pairing, recombination, and bivalent formation, highlighting recent findings on the genetic control and mode of action of specific proteins that lead to diploid-like meiosis behavior in polyploid species. During the meiosis of newly formed polyploids, related chromosomes (homologous in autopolyploids; homologous and homoeologous in allopolyploids) can combine in complex structures called multivalents. These structures occur when multiple chromosomes simultaneously pair, synapse, and recombine. We discuss the effectiveness of crossover frequency in preventing multivalent formation and favoring regular meiosis. Homoeologous recombination in particular can generate new gene (locus) combinations and phenotypes, but it may destabilize the karyotype and lead to aberrant meiotic behavior, reducing fertility. In crop species, understanding the factors that control pairing and recombination has the potential to provide plant breeders with resources to make fuller use of available chromosome variations in number and structure. We focused on wheat and oilseed rape, since there is an abundance of elucidating studies on this subject, including the molecular characterization of the (wheat) and (oilseed rape) loci, which are known to play a crucial role in regulating meiosis. Finally, we exploited the consequences of chromosome pairing and recombination for genetic map construction in polyploids, highlighting two case studies of complex genomes: (i) modern sugarcane, which has a man-made genome harboring two subgenomes with some recombinant chromosomes; and (ii) hexaploid sweet potato, a naturally occurring polyploid. The recent inclusion of allelic dosage information has improved linkage estimation in polyploids, allowing multilocus genetic maps to be constructed.
Topics: Brassica napus; Chromosomes, Plant; Crossing Over, Genetic; Meiosis; Plant Breeding; Polyploidy; Triticum
PubMed: 34680912
DOI: 10.3390/genes12101517 -
The Journal of Cell Biology May 2015Polyploid cells, which contain more than two genome copies, occur throughout nature. Beyond well-established roles in increasing cell size/metabolic output, polyploidy... (Review)
Review
Polyploid cells, which contain more than two genome copies, occur throughout nature. Beyond well-established roles in increasing cell size/metabolic output, polyploidy can also promote nonuniform genome, transcriptome, and metabolome alterations. Polyploidy also frequently confers resistance to environmental stresses not tolerated by diploid cells. Recent progress has begun to unravel how this fascinating phenomenon contributes to normal physiology and disease.
Topics: Animals; Gene Dosage; Genome; Humans; Polyploidy; Transcriptome
PubMed: 26008741
DOI: 10.1083/jcb.201502016 -
Cell Death & Disease May 2017A characteristic cellular feature of the mammalian liver is the progressive polyploidization of the hepatocytes, where individual cells acquire more than two sets of... (Review)
Review
A characteristic cellular feature of the mammalian liver is the progressive polyploidization of the hepatocytes, where individual cells acquire more than two sets of chromosomes. Polyploidization results from cytokinesis failure that takes place progressively during the course of postnatal development. The proportion of polyploidy also increases with the aging process or with cellular stress such as surgical resection, toxic stimulation, metabolic overload, or oxidative damage, to involve as much as 90% of the hepatocytes in mice and 40% in humans. Hepatocyte polyploidization is generally considered an indicator of terminal differentiation and cellular senescence, and related to the dysfunction of insulin and p53/p21 signaling pathways. Interestingly, the high prevalence of hepatocyte polyploidization in the aged mouse liver can be reversed when the senescent hepatocytes are serially transplanted into young mouse livers. Here we review the current knowledge on the mechanism of hepatocytes polyploidization during postnatal growth, aging, and liver diseases. The biologic significance of polyploidization in senescent reversal, within the context of new ways to think of liver aging and liver diseases is considered.
Topics: Aging; Animals; Hepatocytes; Humans; Liver; Polyploidy
PubMed: 28518148
DOI: 10.1038/cddis.2017.167 -
Nature Communications Jun 2023Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows...
Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.
Topics: Genome, Plant; Brassica napus; Genomics; Evolution, Molecular; Polyploidy
PubMed: 37263993
DOI: 10.1038/s41467-023-38560-z