Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum violaceum

Hood, Michael E.; Katawczik, Melanie; Giraud, Tatiana

doi:10.1534/genetics.105.042564

Cited by 73 publications

(79 citation statements)

References 55 publications

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“…In this study, analysis of homologous TEs clearly revealed that U. hordei employs RIP to control TE activity: Numerous point mutations representing C-to-T (G-to-A) transitions were discovered when similar TEs were aligned (see Supplemental Figure 6 online). Many occurred at TCG triplets (or CGA on the opposite strand) as found in a related smut fungus Microbotryum violaceum (Hood et al, 2005), though they were not strictly limited to these triplets as in M. violaceum. This could point to a more complex RIP mechanism than found to date in ascomycetes (Clutterbuck, 2011) or indicate a different mechanism.…”

Section: Genome Defenses Related To Te Control and Heterochromatin Fomentioning

confidence: 91%

Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements

et al. 2012

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Ustilago hordei is a biotrophic parasite of barley (Hordeum vulgare). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb U. hordei genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maizeinfecting smut fungi Ustilago maydis and Sporisorium reilianum but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The U. hordei genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the U. maydis genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in U. maydis. We found evidence of repeat-induced point mutations in the genome of U. hordei, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of U. hordei effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts.

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Section: Genome Defenses Related To Te Control and Heterochromatin Fomentioning

confidence: 91%

Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements

et al. 2012

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“…Secondly, this situation could be realized in other biological processes that may require the pairing of identical sequences, for instance, repeat induced point mutation. 45,46 To probe how the homologous segments recognize each other, we shift the centre of fragment 2 a distance x along the z-axis. Therefore, the centre of fragment 1 lies at z = L/2, whereas that of fragment 2 lies at z = L/2 + x.…”

Section: A General Considerationsmentioning

confidence: 99%

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments

Lee

Wynveen

Albrecht

et al. 2015

The Journal of Chemical Physics

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Homologous gene shuffling between DNA molecules promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition has remained an unsolved puzzle of molecular biology. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has, however, been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular, electrostatic ones. In this proposed mechanism, sequences that have the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts. The difference between the two energies is termed the "recognition energy." Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding is termed the "recognition well." We find there is a recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations and consider more rigorously the optimization of the orientations of the fragments about their long axes upon calculating these recognition energies. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. When torsional flexibility of the DNA molecules is introduced, we find excellent agreement between the analytical approximation and simulations. C 2015 AIP Publishing LLC. [http://dx

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“…In the case of Microbotryum, these include many transposable elements in its genome. Comparative study of the coevolution of transposable elements with fungal genomic defences (repeat induced point mutations; Hood et al, 2005) is another exciting future research area.…”

Section: Biotic Interactions: Microbotryum and The Evolutionary Ecolomentioning

confidence: 99%

Silene as a model system in ecology and evolution

et al. 2009

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The genus Silene, studied by Darwin, Mendel and other early scientists, is re-emerging as a system for studying interrelated questions in ecology, evolution and developmental biology. These questions include sex chromosome evolution, epigenetic control of sex expression, genomic conflict and speciation. Its well-studied interactions with the pathogen Microbotryum has made Silene a model for the evolution and dynamics of disease in natural systems, and its interactions with herbivores have increased our understanding of multi-trophic ecological processes and the evolution of invasiveness. Molecular tools are now providing new approaches to many of these classical yet unresolved problems, and new progress is being made through combining phylogenetic, genomic and molecular evolutionary studies with ecological and phenotypic data. The model role of a non-model organismThe genus Silene (Caryophyllaceae), with a tradition of genetical and ecological studies dating back to Mendel and Darwin, has remarkably many interesting features. First, the species in the genus vary widely in their breeding systems and ecology. Second, several members of this mainly holarctic genus can be easily bred, and have short life cycles, and are thus convenient for experimental and field studies. Genomic resources are now becoming increasingly available in Silene, making genetic, quantitative genetic and molecular studies possible. A strength of Silene as a model system, compared with many classical model organisms, is that researchers can rely on a large number of ecological studies encompassing biotic interactions with sexually transmitted fungi, pollinators and herbivores. It is the wealth of ecological and other earlier knowledge that makes the genus Silene important for studying many biological questions, including the suppression of recombination during sex chromosome evolution, sexually antagonistic selection in an organism that is not an animal, epigenetic processes in flower development, speciation and reproductive isolation, multi-trophic interactions, disease ecology and biological invasions.Thanks to the classical genetic and ecological work on Silene, new progress can now be made in studying some of these important unresolved questions in biology with the aid of modern molecular tools. That new model systems with accessible and well-studied ecology open fruitful avenues for investigation is illustrated also by Mimulus (Wu et al., 2008) and the ongoing efforts to develop genomic resources in an increasing number of different systems. In the following, we outline the unique features of the Silene system, and describe active research areas and future directions, highlighting new advances and work in progress. Evolution of sexual systemsPlants show remarkable diversity in their sexual and mating systems, ranging from hermaphroditism to dioecy, from self-incompatible hermaphroditism to hermaphroditism in which individuals possess a capacity to self-fertilize, but which often show complex mechanisms to promote outcrossing (Darwin, 18...

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Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum violaceum

Cited by 73 publications

References 55 publications

Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements

Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments

Silene as a model system in ecology and evolution

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