Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution

Todd, Robert T.; Forche, Anja; Selmecki, Anna

doi:10.1128/9781555819583.ch28

Cited by 28 publications

(39 citation statements)

References 173 publications

(173 reference statements)

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“…Our analysis and that of others (reviewed in Todd et al, 2017) show that S. cerevisiae strains with higher initial ploidy are also generally more likely to be aneuploid (Figure 3). WGD has played an important role in the diversification and evolution of Saccharomyces yeast (Albertin et al, 2009).…”

Section: Figuresupporting

confidence: 75%

“…The host's attempts at defence include phagocytosis (digestion of cells by phagocytes) and the adaptive immune response, resulting in a stressful situation for the invading pathogen (Romani, 2004). In response, some pathogenic cells change ploidy or become aneuploid upon invasion of their host (reviewed in Todd, Forcher, & Selmecki, 2017).…”

Section: Aneuploidy In Pathogenic Yeastsmentioning

confidence: 99%

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Aneuploidy in yeast: Segregation error or adaptation mechanism?

Gilchrist

Stelkens

2019

Yeast

104

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Aneuploidy is the loss or gain of chromosomes within a genome. It is often detrimental and has been associated with cell death and genetic disorders. However, aneuploidy can also be beneficial and provide a quick solution through changes in gene dosage when cells face environmental stress. Here, we review the prevalence of aneuploidy in Saccharomyces, Candida, and Cryptococcus yeasts (and their hybrid offspring) and analyse associations with chromosome size and specific stressors. We discuss how aneuploidy, a segregation error, may in fact provide a natural route for the diversification of microbes and enable important evolutionary innovations given the right ecological circumstances, such as the colonisation of new environments or the transition from commensal to pathogenic lifestyle. We also draw attention to a largely unstudied cross link between hybridisation and aneuploidy. Hybrid meiosis, involving two divergent genomes, can lead to drastically increased rates of aneuploidy in the offspring due to antirecombination and chromosomal missegregation. Because hybridisation and aneuploidy have both been shown to increase with environmental stress, we believe it important and timely to start exploring the evolutionary significance of their co‐occurrence.

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Section: Figuresupporting

confidence: 75%

Section: Aneuploidy In Pathogenic Yeastsmentioning

confidence: 99%

Aneuploidy in yeast: Segregation error or adaptation mechanism?

Gilchrist

Stelkens

2019

Yeast

104

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“…Failures in kinetochore assembly and attachment increase the probability of chromosome mis-segregation leading to aneuploidy (55). While these drastic genome changes can be detrimental to the organism, formation of aneuploidy and polyploidy is an important strategy orchestrated by pathogens to adapt to the environment during periods of stress (56). Polyploidy and aneuploidy are prevalent in Phytophthora natural isolates and progeny from sexual reproduction (35, 57–60).…”

Section: Discussionmentioning

confidence: 99%

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

Fang

Coelho

Shu

et al. 2019

Preprint

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26Centromeres are chromosomal regions that serve as platforms for kinetochore assembly 27 and spindle attachments, ensuring accurate chromosome segregation during cell division. 28Despite functional conservation, centromere DNA sequences are diverse and often repetitive, 29 making them challenging to assemble and identify. Here, we describe centromeres in an 30 oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and 31 chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput 32 sequencing (ChIP-seq). P. sojae centromeres cluster at a single focus at different life stages and 33 during nuclear division. We report an improved genome assembly of the P. sojae reference strain, 34 which enabled identification of 15 enriched CENP-A binding regions as putative centromeres. 35By focusing on a subset of these regions, we demonstrate that centromeres in P. sojae are 36 regional, spanning 211 to 356 kb. Most of these regions are transposon-rich, poorly transcribed, 37 and lack the histone modification H3K4me2 but are embedded within regions with the 38 heterochromatin marks H3K9me3 and H3K27me3. Strikingly, we discovered a Copia-like 39 transposon (CoLT) that is highly enriched in the CENP-A chromatin. Similar clustered elements 40 are also found in oomycete relatives of P. sojae, and may be applied as a criterion for prediction 41 of oomycete centromeres. This work reveals a divergence of centromere features in oomycetes 42 as compared to other organisms in the Stramenopila-Alveolata-Rhizaria (SAR) supergroup 43 including diatoms and Plasmodium falciparum that have relatively short and simple regional 44 centromeres. Identification of P. sojae centromeres in turn also augments the genome assembly. 45 46 Significance Statement 49Oomycetes are fungal-like microorganisms that belong to the stramenopiles within the 50 Stramenopila-Alveolata-Rhizaria (SAR) supergroup. The Phytophthora oomycetes are infamous 51 as plant killers, threatening crop production worldwide. Because of the highly repetitive nature of 52 their genomes, assembly of oomycete genomes presents challenges that impede identification of 53 centromeres, which are chromosomal sites mediating faithful chromosome segregation. We 54 report long-read sequencing-based genome assembly of the Phytophthora sojae reference strain, 55 which facilitated the discovery of centromeres. P. sojae harbors large regional centromeres 56 enriched for a Copia-like transposon that is also found in discrete clusters in other oomycetes. 57This study provides insight into the oomycete genome organization, and broadens our knowledge 58 of the centromere structure, function and evolution in eukaryotes. 59 60 Accurate segregation of chromosomes during mitosis and meiosis is critical for the 61 development and reproduction of all eukaryotic organisms. Centromeres are specialized regions 62 of chromosomes that mediate kinetochore formation, spindle attachment, and sister chromatid 63 segregation during cell division (1, 2). T...

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“…More than 70% of flowering plants are polyploid (Meyers and Levin 2006) including many crops essential for human consumption and use, including apples, bananas, potatoes, strawberries, and wheat (Renny-Byfield and Wendel 2014). Higher ploidy levels have also been documented in many fungal species (Todd, Forche, and Selmecki 2017). Polyploidy in animals is less common than in these other taxa, but is far from rare, including many species of frogs (Novikova et al 2019), fish (Comber and Smith 2004), crustaceans and molluscs (Goldman, LoVerde, and Chrisman 1983), as well as many species of nematodes (Szitenberg et al 2017).…”

Section: Introductionmentioning

confidence: 99%

GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes

Ranallo-Benavidez

Jaroň

Schatz

2019

Preprint

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An important assessment prior to genome assembly and related analyses is genome profiling, where the k-mer frequencies within raw sequencing reads are analyzed to estimate major genome characteristics such as genome size, heterozygosity, and repetitiveness. Here we introduce GenomeScope 2.0 (https://github.com/tbenavi1/genomescope2.0), which applies combinatorial theory to establish a detailed mathematical model of how k-mer frequencies are distributed in heterozygous and polyploid genomes. We describe and evaluate a practical implementation of the polyploid-aware mixture model that, within seconds, accurately infers genome properties across thousands of simulated and eleven real datasets spanning a broad range of complexity. We also present a new method called Smudgeplots (https://github.com/KamilSJaron/smudgeplot) to visualize and infer the ploidy and genome structure of a genome by analyzing heterozygous k-mer pairs. We successfully apply the approach to systems of known variable ploidy levels in the Meloidogyne genus and also the extreme case of octoploid Fragaria x ananassa.

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Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution

Cited by 28 publications

References 173 publications

Aneuploidy in yeast: Segregation error or adaptation mechanism?

Aneuploidy in yeast: Segregation error or adaptation mechanism?

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes

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