Topic 81

transposable tes te elements element genomes insertions genome transposition silencing insertion genomics evolutionary dna repetitive transposons genomic transposon families species methylation epigenetic drosophila evolution ltr pirna active genes sequences repeat plant content melanogaster suggesting regions variation copy within absence gene de retrotransposons polymorphisms repeats small expression landscape read defense genetic maize host eukaryotic regulation selfish impact evidence they long simulans repression mobile nearby wide eukaryotes their young pirnas thaliana genotypes chromatin retrotransposon silenced deleterious fungal genic contribute patterns rnas sequencing summarytransposable are plants biology contain novo polymorphic mobility assemblies expressed methylated loci mobilization heterochromatin integrity regulate sequence transcript diversification hybrid

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Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon. 81 16 9 5

Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defences 81 40 5

Silencing of Mu elements in maize involves distinct populations of small RNAs and distinct patterns of DNA methylation 81 9

Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression 81 21 5

Genetic and epigenetic contributions to variation in transposable element expression responses to abiotic stress in maize 81 9 5

Transposable element landscape in Drosophila populations selected for longevity 81 21 5

Somatic transposition in the Drosophila intestine occurs in active chromatin and is associated with tumor suppressor gene inactivation 81 9 3

Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita 81 21 5

P-elements strengthen reproductive isolation within the Drosophila simulans species complex 81 21 5

piRNA-mediated silencing of an invading transposable element evolves rapidly through abundant de novo mutations 81 21 5

Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen 81 21 5

Transposon- and genome dynamics in the fungal genus Neurospora: insights from nearly gapless genome assemblies 81 40 5

The effect of hybridization on transposable element accumulation in an undomesticated fungal species 81 21 5

Surprising amount of stasis in repetitive genome content across the Brassicales 81 21 5

Germline gene de-silencing by a transposon insertion is triggered by an altered landscape of local piRNA biogenesis 81 21 9 5

siRNA-mediated de novo silencing of Ac/Ds transposons is initiated by alternative transposition in maize 81 46

Efficient detection of transposable element insertion polymorphisms between genomes using short-read sequencing data 81 25 4

Toxic Y chromosome: increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome 81 56 21 5

Widespread imprinting of transposable elements and young genes in the maize endosperm 81 9 5

Genomic diversity generated by a transposable element burst in a rice recombinant inbred population 81 40 21 5

Transposable Element-Gene Splicing Modulates the Transcriptional Landscape of Human Pluripotent Stem Cells 81 9 3

Cis-regulatory elements within TEs can influence expression of nearby maize genes 81 9 5

Aging leads to stochastic loss of silencing at transposons in mammary luminal epithelial cells 81 31 9 3

Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males 81 56 21 5

Long-Read cDNA Sequencing Enables a 'Gene-Like' Transcript Annotation of Arabidopsis Transposable Elements 81 25 9 4

Transposable element expression at unique loci in single cells with CELLO-seq 81 9 4

Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods 81 40 31 21 9 5

Altering PRC2 activity partially suppresses ddm1 mutant phenotypes in Arabidopsis 93 81 31 16 9 3

Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations 81 21 5

Differential expression of transposable elements in stem cell lineages of the preimplantation embryo 81 20 9 3

Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response in Arabidopsis 81 16 9 3

Novel non-transposable-element regulation patterns of KZFP family reveal new drivers of its rapid evolution 81 40 21 9 5

Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity 81 21 5

Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna 81 21 5

Evolutionary dynamics of transposable elements following a shared polyploidization event in the tribe Andropogoneae 81 40 5

Traces of transposable element in genome dark matter co-opted by flowering gene regulation networks. 81 31 9

Population Level Variation of Transposable Elements in a Maize Diversity Panel 81 25 5

Rapid evolution at the telomere: transposable element dynamics at an intrinsically unstable locus 81 21 5

Ectopic expression of a maize gene is induced by Composite Insertions generated by Alternative Transposition 81 31 9

Evolutionary dynamics of transposable elements in bdelloid rotifers 81 21 5

Unveiling transposable element expression heterogeneity in cell fate regulation at the single-cell level 81 43 31 9 4 3

Evolution of genome structure in the Drosophila simulans species complex 81 40 25 21 5

The plant mobile domain proteins MAIN and MAIL1 interact with the phosphatase PP7L to regulate gene expression and silence transposable elements in Arabidopsis thaliana. 81 16 3

Hybridization history and repetitive element content in the genome of a homoploid hybrid, Yucca gloriosa (Asparagaceae) 81 40 5

The transposable elements of the Drosophila serrata reference panel 81 21 5

The Drosophila TART transposon manipulates the piRNA pathway as a counter-defense strategy to limit host silencing 81 3

Movement of transposable elements contributes to cichlid diversity 81 21 9 5

The impact of transposable elements on tomato diversity 81 19 9 5

A population-level invasion by transposable elements in a fungal pathogen 81 21 5

Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome 81 31 9 3

Genomic re-assessment of the transposable element landscape of the potato genome 81 13 4

Evidence for transposable element control by Argonautes in a parasitic flatworm lacking the piRNA pathway. 81 49 3

Immunity to infections in arboviral vectors by integrated viral sequences: an evolutionary perspective 81 48 21 5

Genetic analysis of hybrid incompatibility suggests transposable elements increase reproductive isolation in the D. virilis clade 81 21 5

HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data 81 25 13 4

Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome 81 21 9 5

Generating high quality assemblies for genomic analysis of transposable elements 81 25 4

The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that direct genome-wide DNA methylation 81 9

Chromatin Regulates Bipartite-Classified Small RNA Expression to Maintain Epigenome Homeostasis in Arabidopsis 81 31 20 16 3

Phenotypic and transcriptomic responses to stress differ according to population geography in an invasive species 81 5

Detailed classification of mariner-like elements, class II transposable elements, in six Apis species based on Dromar 81 40 5

The Enterprise: A massive transposon carrying Spok meiotic drive genes 81 40 5

Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize 81 40 9 5

Transposable elements are constantly exchanged by horizontal transferreshaping mosquito genomes 81 48 40 5

Gene capture by transposable elements leads to epigenetic conflict in maize 81 5

The replicative amplification of MITEs and their impact on rice trait variability 81 19 5

Toxin-antitoxin gene pairs found in Tn3family transposons appear to be an integral part of the transposition module 81 79 12 5

Too much too many: comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats 81 25 5

Evidence-based gene expression modulation correlates with transposable element knock-down 81 16 9 3

Gigantic Genomes Can Provide Empirical Tests of TE Dynamics Models -- An Example from Amphibians 81 40 5

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities 81 56 21 5

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements 81 40 5

Genomic properties of variably methylated retrotransposons in mouse 81 31 9

Tirant stealthily invaded natural Drosophila melanogaster populations during the last century 81 40 5

A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici 81 40 12 5

The tumor suppressor microRNA let-7 inhibits human LINE-1 retrotransposition 81 49 3

Nanopore sequencing enables comprehensive transposable element epigenomic profiling 81 25 9 4

Genome-wide mapping of histone modifications in two species of Leptosphaeria maculans showing contrasting genomic organization and host specialization 81 31 9 5

Gene disruption by structural mutations drives selection in US rice breeding over the last century 53 21 5

Differential chromatin accessibility landscape reveals the structural and functional features of the allopolyploid wheat chromosomes 81 31 9 5

Identification and characterization of retro-DNAs, a new type of retrotransposons originated from DNA transposons, in primate genomes 81 40 9

Transposable element mobilization in interspecific yeast hybrids 81 5

Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukemia 31 9 3

A large accessory genome, high recombination rates, and selection of secondary metabolite genes help maintain global distribution and broad host range of the fungal plant pathogen Claviceps purpurea 21 5

Transposable elements resistant to epigenetic resetting in the human germline are epigenetic hotspots for development and disease 81 20 9

Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade 81 40 21 5

Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks 134 7

Transcript assembly improves expression quantification of transposable elements in single cell RNA-seq data 43 9 3

Chromatin features define adaptive genomic regions in a fungal plant pathogen 93 31 9

Ongoing evolution of KRAB zinc finger protein-coding genes in modern humans 40 21 5

The RNA Polymerase II core subunit RPB-9 directs transcriptional elongation at piRNA loci in Caenorhabditis elegans 90 49 31 20 3

GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data 13 4

Large genomic variants reveal unexplored intraspecific diversity in Brassica rapa genomes 25 7 5

Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows 87 9 5

Full-length LINE-1s with functional ORFs are favoured by host-level selection in human genomes 81 21 5

Transposon mobilization in the human fungal pathogen Cryptococcus deneoformans is mutagenic during infection and promotes drug resistance in vitro 114 12 10 5

Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare. 13 4

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific lineages of the blast fungus 121 40 5

Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish 21 5

TERL: Classification of Transposable Elements by Convolutional Neural Networks 26 4