Keywords: Yeast and Fungi

Evolutionary modes of wtf meiotic driver genes in Schizosaccharomyces pombe

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Yan-Hui Xu, Fang Suo, Xiao-Ran Zhang, et al.,  Genome Biology and Evolution,  2024.
Killer meiotic drivers (KMDs) are a class of selfish genetic elements that bias inheritance in their favor by destroying meiotic progeny that do not carry them. How KMDs evolve is not well understood. In the fission yeast Schizosaccharomyces pombe, the largest gene family, known ...

Rapid, scalable, combinatorial genome engineering by marker-less enrichment and recombination of genetically engineered loci in yeast

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M. Abdullah, B. M. Greco, J. M. Laurent, R. K. Garge, D. R. Boutz, M. Vandeloo, E. M. Marcotte and A. H. Kachroo,  Cell Rep Methods,  3:100464. 2023.
A major challenge to rationally building multi-gene processes in yeast arises due to the combinatorics of combining all of the individual edits into the same strain. Here, we present a precise and multi-site genome editing approach that combines all edits without selection ...

How Selfish Genes Succeed: Critical Insights Uncovered About Dangerous DNA

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STOWERS INSTITUTE FOR MEDICAL RESEARCH,  SciTechDaily,  2022.
New findings from the Stowers Institute for Medical Research uncover critical insights about how a dangerous selfish gene—considered to be a parasitic portion of DNA—functions and survives. Understanding this dynamic is a valuable resource for the broader community studying ...

A Natural Fungal Gene Drive Enacts Killing via DNA Disruption

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A. S. Urquhart and D. M. Gardiner,  mBio,  e0317322. 2022.
Fungal spore killers are a class of selfish genetic elements that positively bias their own inheritance by killing non-inheriting gametes following meiosis. As killing takes place specifically within the developing fungal ascus, a tissue which is experimentally difficult to ...

How selfish genes succeed

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Stowers Institute for Medical Research,  ScienceDaily,  2022.
A new study reveals how a selfish gene in yeast uses a poison-antidote strategy that enables its function and likely has facilitated its long-term evolutionary success. This strategy is an important addition for scientists studying similar systems including teams that are ...

S. pombe wtf drivers use dual transcriptional regulation and selective protein exclusion from spores to cause meiotic drive

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N. L. Nuckolls, A. Nidamangala Srinivasa, A. C. Mok, R. M. Helston, M. A. Bravo Núñez, J. J. Lange, T. J. Gallagher, C. W. Seidel and S. E. Zanders,  PLOS Genetics,  18:e1009847. 2022.
Author summary Genomes are often considered a collection of ‘good’ genes that provide beneficial functions for the organism. From this perspective, disease is thought to arise due to disfunction of ‘good’ genes. For example, infertility can be caused by the failure of a ...

Engineering stringent genetic biocontainment of yeast with a protein stability switch

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S. A. Hoffmann and Y. Cai,  bioRxiv,  2022.11.24.517818. 2022.
Synthetic biology holds immense promise to tackle key problems we are facing, for instance in resource use, environmental health, and human health care. However, comprehensive safety measures are needed to deploy genetically engineered microorganisms in open-environment ...

Discovery of 119-Million-Year-Old “Selfish” Genes Casts Doubt on Established Evolution Beliefs

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Stowers Institute for Medical Research,  SciTechDaily,  2022.
Meiotic drivers, a kind of selfish gene, are indeed selfish. They are found in virtually all species’ genomes, including humans, and unjustly transfer their genetic material to more than half of their offspring, resulting in infertility and impaired organism health. Their ...

Gene drive by Fusarium SKC1 is dependent on its competing allele

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J. M. Lohmar, N. A. Rhoades, T. M. Hammond and D. W. Brown,  Fungal Genetics and Biology,  163:103749. 2022.
The Fusarium verticillioides SKC1 gene driver is transmitted to offspring in a biased manner through spore killing. The mechanism that allows SKC1 to kill non-SKC1 offspring while sparing others is poorly understood. Here we report that gene drive by SKC1 is dependent on SKC1's ...

119-Million-Year-Old “Selfish” Genes Uncovered in Yeast

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Stowers Institute for Medical Research,  Technology Networks,  2022.
Meiotic drivers, a type of selfish gene, are indeed selfish. Present in the genomes of nearly all species, including humans, they unfairly transfer their genetic material to more than half of their offspring, sometimes leading to infertility, and decreased organism health. ...

The wtf meiotic driver gene family has unexpectedly persisted for over 100 million years

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M. De Carvalho, G. S. Jia, A. Nidamangala Srinivasa, R. B. Billmyre, Y. H. Xu, J. J. Lange, I. M. Sabbarini, L. L. Du and S. E. Zanders,  eLife,  11. 2022.
Meiotic drivers are selfish elements that bias their own transmission into more than half of the viable progeny produced by a driver+/driver- heterozygote. Meiotic drivers are thought to exist for relatively short evolutionary timespans because a driver gene or gene family is ...

Meiotic drive is associated with sexual incompatibility in Neurospora

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A. Vogan, J. Svedberg, M. Grudzinska-Sterno and H. Johannesson,  Evolution,  2022.
Evolution of Bateson-Dobzhansky-Muller (BDM) incompatibilities is thought to represent a key step in the formation of separate species. They are incompatible alleles that have evolved in separate populations and are exposed in hybrid offspring as hybrid sterility or lethality. In ...

Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom

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J. Y. Chou, P. C. Hsu and J. Y. Leu,  Microbiology and Molecular Biology Reviews,  2022.
Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various ...

On the Mechanistic Basis of Killer Meiotic Drive in Fungi

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S. J. Saupe and H. Johannesson,  Annual Review of Microbiology,  76:305-323. 2022.
Spore killers are specific genetic elements in fungi that kill sexual spores that do not contain them. A range of studies in the last few years have provided the long-awaited first insights into the molecular mechanistic aspects of spore killing in different fungal models, ...

Non-Mendelian transmission of accessory chromosomes in fungi

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J. Komluski, E. H. Stukenbrock and M. Habig,  Chromosome Research,  2022.
Non-Mendelian transmission has been reported for various genetic elements, ranging from small transposons to entire chromosomes. One prime example of such a transmission pattern are B chromosomes in plants and animals. Accessory chromosomes in fungi are similar to B chromosomes ...

Isolation of rfk-2 (UV) , a mutation that blocks spore killing by Neurospora Spore killer-3

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A. Velazquez, E. Webber, D. O'Neil, T. Hammond and N. Rhoades,  MicroPublication Biology,  2022.
Neurospora Spore killer-3 ( Sk-3 ) is a selfish genetic element that kills spores to achieve gene drive.  Here, to help identify Sk-3’s killer, we performed a genetic screen for required for killing (rfk) mutations (see methods). The genetic screen uses Sk‑3 rskΔ × SkS ...

A-to-I mRNA editing controls spore death induced by a fungal meiotic drive gene in homologous and heterologous expression systems

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J. M. Lohmar, N. A. Rhoades, T. N. Patel, R. H. Proctor, T. M. Hammond and D. W. Brown,  Genetics,  2022.
Spore killers are meiotic drive elements that can block development of sexual spores in fungi. In the maize ear rot and mycotoxin-producing fungus Fusarium verticillioides, a spore killer called SkK has been mapped to a 102-kb interval of chromosome V. Here, we show that a gene ...

The spore killers, fungal meiotic driver elements

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A. A. Vogan, I. Martinossi-Allibert, S. L. Ament-Velásquez, J. Svedberg and H. Johannesson,  Mycologia,  2022.
During meiosis, both alleles of any given gene should have equal chances of being inherited by the progeny. There are a number of reasons why, however, this is not the case, with one of the most intriguing instances presenting itself as the phenomenon of meiotic drive. Genes that ...

A natural fungal gene drive enacts killing through targeting DNA

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A. S. Urquhart and D. M. Gardiner,  bioRxiv,  2022.01.19.477016. 2022.
Fungal spore-killers are a class of selfish genetic elements that positively bias their own inheritance by killing non-inheriting gametes following meiosis. As killing takes place specifically within the developing fungal ascus, a tissue which is experimentally difficult to ...

Analysis of a Cas12a-based gene-drive system in budding yeast

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I. C. Lewis, Y. Yan and G. C. Finnigan,  Access Microbiol,  3:000301. 2022.
The discovery and adaptation of CRISPR/Cas systems within molecular biology has provided advances across biological research, agriculture and human health. Genomic manipulation through use of a CRISPR nuclease and programmed guide RNAs has become a common and widely accessible ...

Molecular Mechanisms and Evolutionary Consequences of Spore Killers in Ascomycetes

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S. Zanders and H. Johannesson,  Microbiology and Molecular Biology Reviews,  2021.
In this review, we examine the fungal spore killers. These are meiotic drive elements that cheat during sexual reproduction to increase their transmission into the next generation. Spore killing has been detected in a number of ascomycete genera, including Podospora, Neurospora, ...

Versatile Applications of the CRISPR/Cas Toolkit in Plant Pathology and Disease Management

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M. S. Wheatley and Y. N. Yang,  Phytopathology,  111:1080-1090. 2021.
New tools and advanced technologies have played key roles in facilitating basic research in plant pathology and practical approaches for disease management and crop health. Recently. the CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR-associated) ...

An introgressed gene causes meiotic drive in Neurospora sitophila

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J. Svedberg, A. A. Vogan, N. A. Rhoades, D. Sarmarajeewa, D. J. Jacobson, M. Lascoux, T. M. Hammond and H. Johannesson,  Proceedings of the National Academy of Sciences of the United States of America,  118:9. 2021.
Meiotic drive elements cause their own preferential transmission following meiosis. In fungi, this phenomenon takes the shape of spore killing, and in the filamentous ascomycete Neurospora sitophila, the Sk-1 spore killer element is found in many natural populations. In this ...

Developing GDi-CRISPR System for Multi-copy Integration in Saccharomyces cerevisiae

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Z.-X. Zhang, Y.-Z. Wang, Y.-S. Xu, X.-M. Sun and H. Huang,  Applied Biochemistry and Biotechnology,  2021.
This study aims to develop a low-cost and easy-to-use multi-copy integration tool in S. cerevisiae. Firstly, twenty-one Cas proteins from different microorganisms were tested in S. cerevisiae to find the functional Cas proteins with optimal cleavage ability. Results showed that ...

RNA editing controls meiotic drive by a Neurospora Spore killer

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N. A. Rhoades and T. M. Hammond,  bioRxiv,  2020.12.30.424869. 2021.
Neurospora Sk-2 is a complex meiotic drive element that is transmitted to offspring through sexual reproduction in a biased manner. Sk-2’s biased transmission mechanism involves spore killing, and recent evidence has demonstrated that spore killing is triggered by a gene called ...

Vector dynamics influence spatially imperfect genetic interventions against disease

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M. K. Yuksel, C. H. Remien, B. Karki, J. J. Bull and S. M. Krone,  Evolution, Medicine, and Public Health,  9:1-10. 2020.
In spatially structured populations, imperfect coverage of the vector will leave pockets in which the parasite may persist. Movement by humans may disrupt this local persistence and facilitate eradication when these pockets are small, spreading parasite reproduction outside ...

Chromosome drives via CRISPR-Cas9 in yeast

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H. Xu, M. Han, S. Zhou, B.-Z. Li, Y. Wu and Y.-J. Yuan,  Nature Communications,  11:4344. 2020.
Our results show that the entire Saccharomyces cerevisiae chromosome can be eliminated efficiently through only one double-strand break around the centromere via CRISPR-Cas9. As a proof-of-concept experiment of this CRISPR-Cas9 chromosome drive system, the synthetic yeast ...

Survival of the fit-ish

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Stowers Institute for Medical Research,  Science Daily,  2020.
In a paper published online August 13, 2020, in eLife, members of the Zanders lab explain how it could be possible that meiotic drivers persist in the population, even as they kill off many would-be hosts. It turns out that S. pombe can employ variants of other genes to help ...

Atypical meiosis can be adaptive in outcrossed Schizosaccharomyces pombe due to wtf meiotic drivers

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M. A. Bravo Núñez, I. M. Sabbarini, L. E. Eide, R. L. Unckless and S. E. Zanders,  eLife,  9:e57936. 2020.
Here, we demonstrate that in scenarios analogous to outcrossing, wtf drivers generate a fitness landscape in which atypical spores, such as aneuploids and diploids, are advantageous. In this context, wtf drivers can decrease the fitness costs of mutations that disrupt meiotic ...

Invasion and maintenance of spore killers in populations of ascomycete fungi

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I. Martinossi-Allibert, C. Veller, S. L. Ament-Velásquez, A. A. Vogan, C. Rueffler and H. Johannesson,  bioRxiv,  2020.04.06.026989. 2020.
We show how ploidy level, rate of selfing, and efficiency of spore killing affect the invasion probability of a driving allele and the conditions for its stable coexistence with the non-driving allele. Our model can be adapted to different fungal life-cycles, and is applied here ...

The Enterprise: A massive transposon carrying Spokt meiotic drive genes

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A. A. Vogan, S. L. Ament-Velásquez, E. Bastiaans, O. Wallerman, S. J. Saupe, A. Suh and H. Johannesson,  bioRxiv,  2020.03.25.007153. 2020.
Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive genes of the Spok gene family. The Spok block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within P. ...

The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family

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A. Y. Coughlan, L. Lombardi, S. Braun-Galleani, A. A. R. Martos, V. Galeote, F. Bigey, S. Dequin, K. P. Byrne and K. H. Wolfe,  eLife,  9:e55336. 2020.
The mating-type switching endonuclease HO plays a central role in the natural life cycle of Saccharomyces cerevisiae, but its evolutionary origin is unknown. HO is a recent addition to yeast genomes, present in only a few genera close to Saccharomyces. Here we show that HO is ...

Controversial ‘gene drive’ could disarm deadly wheat pathogen

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Elizabeth Pennisi,  Science,  2020.
The Fusarium fungus is the bane of every wheat farmer’s existence. Causing wheat scab—also known as head blight—it decimates harvests and contaminates grains with a toxin harmful to people and animals. Now, Australian researchers have come up with a new strategy to combat ...

Natural gene drives offer potential pathogen control strategies in plants

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D. M. Gardiner, A. Rusu, L. Barrett, G. C. Hunter and K. Kazan,  bioRxiv,  2020.
Globally, fungal pathogens cause enormous crop losses and current control practices are not always effective, economical or environmentally sustainable. Tools enabling genetic management of wild pathogen populations could potentially solve many problems associated with plant ...

Dramatically diverse Schizosaccharomyces pombe wtf meiotic drivers all display high gamete-killing efficiency

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M. A. Bravo Núñez, I. M. Sabbarini, M. T. Eickbush, Y. Liang, J. J. Lange, A. M. Kent and S. E. Zanders,  PLOS Genetics,  16:e1008350. 2020.
During gametogenesis, the two gene copies at a given locus, known as alleles, are each transmitted to 50% of the gametes (e.g. sperm). However, some alleles cheat so that they are found in more than the expected 50% of gametes, often at the expense of fertility. This selfish ...

An introgressed gene causes meiotic drive in Neurospora sitophila

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J. Svedberg, A. A. Vogan, N. A. Rhoades, D. Sarmarajeewa, D. J. Jacobson, M. Lascoux, T. M. Hammond and H. Johannesson,  bioRxiv,  2020.01.29.923946. 2020.
In this study, we identify the gene responsible for spore killing in Sk-1 by generating both long and short-read genomic data and by using these data to perform a genome wide association test. By phylogenetic analysis, we demonstrate that the gene is likely to have been ...

Combinations of Spok genes create multiple meiotic drivers in Podospora

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A. A. Vogan, S. L. Ament-Velásquez, A. Granger-Farbos, J. Svedberg, E. Bastiaans, A. J. M. Debets, V. Coustou, H. Yvanne, C. Clavé, S. J. Saupe and H. Johannesson,  eLife,  8:e46454. 2019.
Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical ...

A family of killers

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M. De Carvalho and S. E. Zanders,  eLife,  8:e49211. 2019.
Spok genes are meiotic drivers that increase their own chances of transmission by killing gametes that do not inherit them.

Identification of fk-1;, a Meiotic Driver Undergoing RNA Editing in Neurospora

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N. A. Rhoades, A. M. Harvey, D. A. Samarajeewa, J. Svedberg, A. Yusifov, A. Abusharekh, P. Manitchotpisit, D. W. Brown, K. J. Sharp, D. G. Rehard, J. Peters, X. Ostolaza-Maldonado, J. Stephenson, P. K. T. Shiu, H. Johannesson and T. M. Hammond,  Genetics,  212:93. 2019.
These findings indicate that unedited and edited rfk-1 transcripts exist and that these transcripts could have different roles with respect to the mechanism of meiotic drive by spore killing. Regardless of RNA editing, spore killing only succeeds if rfk-1 transcripts avoid ...

Modulating CRISPR gene drive activity through nucleocytoplasmic localization of Cas9 in S. cerevisiae

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M. E. Goeckel, E. M. Basgall, I. C. Lewis, S. C. Goetting, Y. Yan, M. Halloran and G. C. Finnigan,  Fungal Biology Biotechnology,  6:2. 2019.
In this study, we use artificial gene drives in budding yeast to explore mechanisms to modulate nuclease activity of Cas9 through its nucleocytoplasmic localization. We examine non-native nuclear localization sequences (both NLS and NES) on Cas9 fusion proteins in vivo through ...

A Multiple Gene Drive System

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Ferdinand Nanfack Minkeu,  IGTRCN,  2019.
Yan & Finnigan, (2018) recently published a paper in Scientific Reports describing an artificial multi-locus gene drive system by using a single Cas9 and three guide RNA (gRNA) in the budding yeast Saccharomyces cerevisiae. Nuclease-based gene drives do not follow the typical ...

Gene drive inhibition by the anti-CRISPR proteins AcrIIA2 and AcrIIA4 in Saccharomyces cerevisiae

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Basgall, EMG, S. C.; Goeckel, M. E.; Giersch, R. M.; Roggenkamp, E.; Schrock, M. N.; Halloran, M.; Finnigan, G. C.,  Microbiology-Sgm,  164:464-474. 2018.
Given the widespread use and application of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas gene editing system across many fields, a major focus has been the development, engineering and discovery of molecular means to precisely control and regulate ...

Development of a multi-locus CRISPR gene drive system in budding yeast

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Yan, YF, Gregory C.,  Scientific reports,  8:17277-17277. 2018.
The discovery of CRISPR/Cas gene editing has allowed for major advances in many biomedical disciplines and basic research. One arrangement of this biotechnology, a nuclease-based gene drive, can rapidly deliver a genetic element through a given population and studies in fungi and ...

Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast

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Zanders, SEE, M. T.; Yu, J. S.; Kang, J. W.; Fowler, K. R.; Smith, G. R.; Malik, H. S.,  eLife,  3:e02630. 2014.
Hybrid sterility is one of the earliest postzygotic isolating mechanisms to evolve between two recently diverged species. Here we identify causes underlying hybrid infertility of two recently diverged fission yeast species Schizosaccharomyces pombe and S. kambucha, which mate to ...

Rapid evolution of yeast centromeres in the absence of drive

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Bensasson, DZ, M.; Burt, A.; Koufopanou, V.,  Genetics,  178:2161-2167. 2008.
To find the most rapidly evolving regions in the yeast genome we compared most of chromosome III from three closely related lineages of the wild yeast Saccharomyces paradoxits. Unexpectedly, the centromere appears to be the fastest-evolving part of the chromosome, evolving even ...

Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species

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Posey, KLK, V.; Burt, A.; Gimble, F. S.,  Nucleic Acids Research,  32:3947-3956. 2004.
Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit to their host. They encode site-specific DNA endonucleases that perpetuate the element within a species population by homing and disseminate it between species by horizontal transfer. ...

Homing endonuclease genes: the rise and fall and rise again of a selfish element

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Burt, AK, V.,  Current Opinion in Genetics & Development,  14:609-615. 2004.
Homing endonuclease genes (HEGs) are selfish genetic elements that spread by first cleaving chromosomes that do not contain them and then getting copied across to the broken chromosome as a byproduct of the repair process. The success of this strategy will depend on the ...

Analysis of two additional loci in Neurospora crassa related to Spore killer-2

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Turner, BC,  Fungal Genetics and Biology,  39:142-150. 2003.
Two new loci found in one strain of Neurospora crassa (P2604) collected in Malaya are related to the meiotic drive system Spore killer Sk-2. Sk-2 was found in Neurospora intermedia and introgressed into N. crassa. P2604 showed high resistance to killing when crossed to Sk-2. This ...

Adaptation for horizontal transfer in a homing endonuclease

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Koufopanou, VG, M. R.; Burt, A.,  Molecular Biology and Evolution,  19:239-246. 2002.
Selfish genes of no function other than self-propagation are susceptible to degeneration if they become fixed in a population. and regular transfer to new species may be the only means for their long-term persistence. To test this idea we surveyed 24 species of yeast for VDE, a ...

Outcrossed sex allows a selfish gene to invade yeast populations

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Goddard, MRG, D.; Burt, A.,  Proceedings of the Royal Society B-Biological Sciences,  268:2537-2542. 2001.
Homing endonuclease genes (HEGs) in eukaryotes are optional genes that have no obvious effect on host phenotype except for causing chromosomes not containing a cop), of the gene to be cut, thus causing them to be inherited at a greater than Mendelian rate via gene conversion. ...

Recurrent invasion and extinction of a selfish gene

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Goddard, MRB, A.,  Proceedings of the National Academy of Sciences of the United States of America,  96:13880-13885. 1999.
Homing endonuclease genes show super-Mendelian inheritance, which allows them to spread in populations even when they are of no benefit to the host organism. To test the idea that regular horizontal transmission is necessary for the long-term persistence of these genes, we ...