Transposable Elements and Genome Evolution
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Transposable element islands facilitate adaptation to novel environments in an invasive species : Nature Communications : Nature Publishing Group

Transposable element islands facilitate adaptation to novel environments in an invasive species : Nature Communications : Nature Publishing Group | Transposable Elements and Genome Evolution | Scoop.it
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Widespread Genome Reorganization of an Obligate Virus Mutualist

Widespread Genome Reorganization of an Obligate Virus Mutualist | Transposable Elements and Genome Evolution | Scoop.it
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An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons : Nature : Nature Publishing Group

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons : Nature : Nature Publishing Group | Transposable Elements and Genome Evolution | Scoop.it
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The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development: Cell

The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development: Cell | Transposable Elements and Genome Evolution | Scoop.it
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Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming

Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming | Transposable Elements and Genome Evolution | Scoop.it
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Genome Biology | Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content

Genome Biology | Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content | Transposable Elements and Genome Evolution | Scoop.it

We investigated how an extremely transposon element (TE)-rich organism such as the plant-symbiotic ascomycete truffle Tuber melanosporum exploits DNA methylation to cope with the more than 45,000 repeated elements that populate its genome.

Whole-genome bisulfite sequencing performed on different developmental stages reveals a high fraction of methylated cytosines with a strong preference for CpG sites. The methylation pattern is highly similar among samples and selectively targets TEs rather than genes. A marked trend toward hypomethylation is observed for TEs located within a 1 kb distance from expressed genes, rather than segregated in TE-rich regions of the genome. Approximately 300 hypomethylated or unmethylated TEs are transcriptionally active, with higher expression levels in free-living mycelium compared to fruitbody. Indeed, multiple TE-enriched, copy number variant regions bearing a significant fraction of hypomethylated and expressed TEs are found almost exclusively in free-living mycelium. A reduction of DNA methylation, restricted to non-CpG sites and accompanied by an increase in TE expression, is observed upon treatment of free-living mycelia with 5-azacytidine.

 

Conclusions. Evidence derived from analysis of the T. melanosporum methylome indicates that a non-exhaustive, partly reversible, methylation process operates in truffles. This allows for the existence of hypomethylated, transcriptionally active TEs that are associated with copy number variant regions of the genome. Non-exhaustive TE methylation may reflect a role of active TEs in promoting genome plasticity and the ability to adapt to sudden environmental changes.


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Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting | Transposable Elements and Genome Evolution | Scoop.it
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Speciation in Fungal and Oomycete Plant Pathogens - Annual Review of Phytopathology, 52(1):289

Speciation in Fungal and Oomycete Plant Pathogens - Annual Review of Phytopathology, 52(1):289 | Transposable Elements and Genome Evolution | Scoop.it
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Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates

Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates | Transposable Elements and Genome Evolution | Scoop.it
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Antifungal drug resistance evoked via RNAi-dependent epimutations : Nature : Nature Publishing Group

Antifungal drug resistance evoked via RNAi-dependent epimutations : Nature : Nature Publishing Group | Transposable Elements and Genome Evolution | Scoop.it
Microorganisms evolve via a range of mechanisms that may include or involve sexual/parasexual reproduction, mutators, aneuploidy, Hsp90 and even prions. Mechanisms that may seem detrimental can be repurposed to generate diversity. Here we show that the human fungal pathogen Mucor circinelloides develops spontaneous resistance to the antifungal drug FK506 (tacrolimus) via two distinct mechanisms. One involves Mendelian mutations that confer stable drug resistance; the other occurs via an epigenetic RNA interference (RNAi)-mediated pathway resulting in unstable drug resistance. The peptidylprolyl isomerase FKBP12 interacts with FK506 forming a complex that inhibits the protein phosphatase calcineurin. Calcineurin inhibition by FK506 blocks M. circinelloides transition to hyphae and enforces yeast growth. Mutations in the fkbA gene encoding FKBP12 or the calcineurin cnbR or cnaA genes confer FK506 resistance and restore hyphal growth. In parallel, RNAi is spontaneously triggered to silence the fkbA gene, giving rise to drug-resistant epimutants. FK506-resistant epimutants readily reverted to the drug-sensitive wild-type phenotype when grown without exposure to the drug. The establishment of these epimutants is accompanied by generation of abundant fkbA small RNAs and requires the RNAi pathway as well as other factors that constrain or reverse the epimutant state. Silencing involves the generation of a double-stranded RNA trigger intermediate using the fkbA mature mRNA as a template to produce antisense fkbA RNA. This study uncovers a novel epigenetic RNAi-based epimutation mechanism controlling phenotypic plasticity, with possible implications for antimicrobial drug resistance and RNAi-regulatory mechanisms in fungi and other eukaryotes.
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Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the smut fungus Melanopsichium pennsylvanicum

Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the smut fungus Melanopsichium pennsylvanicum | Transposable Elements and Genome Evolution | Scoop.it

Smut fungi are well-suited to investigate the ecology and evolution of plant pathogens, as they are strictly biotrophic, yet cultivable on media. Here we report the genome sequence of Melanopsichium pennsylvanicum, closely related to Ustilago maydis and other Poaceae-infecting smuts, but parasitic to a dicot plant. To explore the evolutionary patterns resulting from host adaptation after this huge host jump, the genome of M. pennsylvanicum was sequenced and compared to the genomes of Ustilago maydis, Sporisorium reilianum, and Ustilago hordei. While all four genomes had a similar completeness in CEGMA analyses, gene absence was highest in M. pennsylvanicum, and most pronounced in putative secreted proteins, which are often considered as effector candidates. In contrast, the amount of private genes was similar among the species, highlighting that gene loss rather than gene gain is the hallmark of adaptation after the host jump to the dicot host. Our analyses revealed a trend of putative effectors to be next to another putative effector, but the majority of these are not in clusters and thus the focus on pathogenicity clusters might not be appropriate for all smut genomes. Positive selection studies revealed that M. pennsylvanicum has the highest number and proportion of genes under positive selection. In general, putative effectors showed a higher proportion of positively selected genes than non-effector candidates. The 248 putative secreted effectors found in all four smut genomes might constitute a core set needed for pathogenicity, while those 92 that are found in all grass-parasitic smuts, but have no ortholog in M. pennsylvanicum might constitute a set of effectors important for successful colonization of grass hosts.


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Directional selection can drive the evolution of modularity in complex traits

Directional selection can drive the evolution of modularity in complex traits | Transposable Elements and Genome Evolution | Scoop.it
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Escape from bacterial iron piracy through rapid evolution of transferrin

Escape from bacterial iron piracy through rapid evolution of transferrin | Transposable Elements and Genome Evolution | Scoop.it
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Coevolution Drives the Emergence of Complex Traits and Promotes Evolvability

Coevolution Drives the Emergence of Complex Traits and Promotes Evolvability | Transposable Elements and Genome Evolution | Scoop.it
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.
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Evolutionary transitions in individuality: insights from transposable elements

Evolutionary transitions in individuality: insights from transposable elements | Transposable Elements and Genome Evolution | Scoop.it
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Microbial genome-enabled insights into plant-microorganism interactions : Nature Reviews Genetics : Nature Publishing Group

Microbial genome-enabled insights into plant-microorganism interactions : Nature Reviews Genetics : Nature Publishing Group | Transposable Elements and Genome Evolution | Scoop.it
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Bistable Expression of Virulence Genes in Salmonella Leads to the Formation of an Antibiotic-Tolerant Subpopulation

Bistable Expression of Virulence Genes in Salmonella Leads to the Formation of an Antibiotic-Tolerant Subpopulation | Transposable Elements and Genome Evolution | Scoop.it
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.
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Disputed genomic islands

Disputed genomic islands | Transposable Elements and Genome Evolution | Scoop.it
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Even though Hahn continues to look for islands, he and other skeptics are not convinced. But others say Nosil's and Wolf's results, and similar recent work, are keeping the idea of genomic islands afloat. “Things will become clearer as we get more sophisticated about the analysis and get more samples,” says Nicholas Barton, an evolutionary biologist at the University of Edinburgh in the United Kingdom. “But it will be a long time.” For now, fans and foes of genomic islands remain oceans apart.

  
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eQTL Mapping of Transposon Silencing Reveals a Position-Dependent Stable Escape from Epigenetic Silencing and Transposition of AtMu1 in the Arabidopsis Lineage

eQTL Mapping of Transposon Silencing Reveals a Position-Dependent Stable Escape from Epigenetic Silencing and Transposition of AtMu1 in the Arabidopsis Lineage | Transposable Elements and Genome Evolution | Scoop.it
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Horizontal Gene Transfer in Eukaryotic Plant Pathogens - Annual Review of Phytopathology, 52(1):583

Horizontal Gene Transfer in Eukaryotic Plant Pathogens - Annual Review of Phytopathology, 52(1):583 | Transposable Elements and Genome Evolution | Scoop.it
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Harnessing Population Genomics to Understand How Bacterial Pathogens Emerge, Adapt to Crop Hosts, and Disseminate - Annual Review of Phytopathology, 52(1):19

Harnessing Population Genomics to Understand How Bacterial Pathogens Emerge, Adapt to Crop Hosts, and Disseminate - Annual Review of Phytopathology, 52(1):19 | Transposable Elements and Genome Evolution | Scoop.it
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Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots

Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots | Transposable Elements and Genome Evolution | Scoop.it
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Burgeoning evidence indicates that microRNAs were initially formed from transposable element sequences

Burgeoning evidence indicates that microRNAs were initially formed from transposable element sequences | Transposable Elements and Genome Evolution | Scoop.it
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