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

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s10577-012-9290-3openalex-snapshot

Centromeres of filamentous fungi

inferredcites →https://doi.org/10.1016/0092-8674(94)90180-5openalex-snapshot

Position effect variegation at fission yeast centromeres

inferredcites →https://doi.org/10.1016/j.cell.2008.03.029openalex-snapshot

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

inferredcites →https://doi.org/10.1016/j.gde.2005.02.003openalex-snapshot

Controlling DNA methylation: many roads to one modification

inferredcites →https://doi.org/10.1016/j.pbi.2015.05.033openalex-snapshot

Small RNAs — the secret agents in the plant–pathogen interactions

inferredcites →https://doi.org/10.1016/j.tig.2019.07.007openalex-snapshot

DNA Methylation: Shared and Divergent Features across Eukaryotes

inferredcites →https://doi.org/10.1016/s0168-9525(00)02024-2openalex-snapshot

EMBOSS: The European Molecular Biology Open Software Suite

inferredcites →https://doi.org/10.1023/a:1022815931524openalex-snapshot

RNA interference is required for normal centromere function infission yeast

inferredcites →https://doi.org/10.1038/nature25027openalex-snapshot

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs

inferredcites →https://doi.org/10.1038/ncomms5104openalex-snapshot

Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

inferredcites →https://doi.org/10.1038/nmeth.3317openalex-snapshot

HISAT: a fast spliced aligner with low memory requirements

inferredcites →https://doi.org/10.1038/nmeth.4184openalex-snapshot

Detecting DNA cytosine methylation using nanopore sequencing

inferredcites →https://doi.org/10.1038/nplants.2016.163openalex-snapshot

Non-canonical RNA-directed DNA methylation

inferredcites →https://doi.org/10.1038/nrg2916openalex-snapshot

Small RNA sorting: matchmaking for Argonautes

inferredcites →https://doi.org/10.1038/nrg3683openalex-snapshot

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

inferredcites →https://doi.org/10.1038/nrm4085openalex-snapshot

The expanding world of small RNAs in plants

inferredcites →https://doi.org/10.1038/nrmicro2790openalex-snapshot

Genome evolution in filamentous plant pathogens: why bigger can be better

inferredcites →https://doi.org/10.1038/s41467-017-02525-wopenalex-snapshot

High-resolution TADs reveal DNA sequences underlying genome organization in flies

inferredcites →https://doi.org/10.1038/s41467-019-12927-7openalex-snapshot

Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation

inferredcites →https://doi.org/10.1038/s41559-019-0810-9openalex-snapshot

Diversity of cytosine methylation across the fungal tree of life

inferredcites →https://doi.org/10.1073/pnas.1019315108openalex-snapshot

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

inferredcites →https://doi.org/10.1073/pnas.1713725115openalex-snapshot

RNAi is a critical determinant of centromere evolution in closely related fungi

inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot

edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/bts311openalex-snapshot

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets

inferredcites →https://doi.org/10.1093/bioinformatics/bty149openalex-snapshot

NanoPack: visualizing and processing long-read sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot

Minimap2: pairwise alignment for nucleotide sequences

inferredcites →https://doi.org/10.1093/dnares/dsy016openalex-snapshot

Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle

inferredcites →https://doi.org/10.1093/gbe/evaa071openalex-snapshot

Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat

inferredcites →https://doi.org/10.1093/molbev/msw046openalex-snapshot

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot

MUSCLE: multiple sequence alignment with high accuracy and high throughput

inferredcites →https://doi.org/10.1093/nar/gkn176openalex-snapshot

High-throughput functional annotation and data mining with the Blast2GO suite

inferredcites →https://doi.org/10.1093/nar/gku1063openalex-snapshot

Rfam 12.0: updates to the RNA families database

inferredcites →https://doi.org/10.1093/nar/gkv424openalex-snapshot

Accurate identification of centromere locations in yeast genomes using Hi-C

inferredcites →https://doi.org/10.1093/nar/gky316openalex-snapshot

psRNATarget: a plant small RNA target analysis server (2017 release)

inferredcites →https://doi.org/10.1098/rstb.2004.1611openalex-snapshot

The role of heterochromatin in centromere function

inferredcites →https://doi.org/10.1101/094672openalex-snapshot

De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing

inferredcites →https://doi.org/10.1101/cshperspect.a017921openalex-snapshot

Neurospora crassa, a Model System for Epigenetics Research

inferredcites →https://doi.org/10.1101/cshperspect.a019323openalex-snapshot

RNAi and Heterochromatin Assembly

inferredcites →https://doi.org/10.1101/gad.9.2.218openalex-snapshot

Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation.

inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot

Circos: An information aesthetic for comparative genomics

inferredcites →https://doi.org/10.1101/gr.849004openalex-snapshot

WebLogo: A Sequence Logo Generator: Figure 1

inferredcites →https://doi.org/10.1111/j.1364-3703.2005.00273.xopenalex-snapshot

Stem rust of small grains and grasses caused by Puccinia graminis

inferredcites →https://doi.org/10.1111/j.1365-2958.1992.tb02202.xopenalex-snapshot

Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences

inferredcites →https://doi.org/10.1111/j.1536-7150.1996.tb02648.xopenalex-snapshot

International Food Policy Research Institute

inferredcites →https://doi.org/10.1111/mpp.12499openalex-snapshot

Epigenetic regulation of development and pathogenesis in fungal plant pathogens

inferredcites →https://doi.org/10.1111/mpp.12841openalex-snapshot

Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance

inferredcites →https://doi.org/10.1111/nph.15432openalex-snapshot

DNA methylation dynamics during the interaction of wheat progenitor Aegilops tauschii with the obligate biotrophic fungus Blumeria graminis f. sp. tritici

inferredcites →https://doi.org/10.1126/science.1062939openalex-snapshot

The Centromere Paradox: Stable Inheritance with Rapidly Evolving DNA

inferredcites →https://doi.org/10.1126/science.1074973openalex-snapshot

Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi

inferredcites →https://doi.org/10.1126/science.1076446openalex-snapshot

El Nino Events Recorded by Stalagmite Carbon Isotopes

inferredcites →https://doi.org/10.1126/science.1239705openalex-snapshot

Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways

inferredcites →https://doi.org/10.1126/science.aao4810openalex-snapshot

Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat

inferredcites →https://doi.org/10.1126/science.aar4142openalex-snapshot

Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes

inferredcites →https://doi.org/10.1128/mbio.01581-19openalex-snapshot

Cellular Dynamics and Genomic Identity of Centromeres in Cereal Blast Fungus

inferredcites →https://doi.org/10.1128/mbio.02275-17openalex-snapshot

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity

inferredcites →https://doi.org/10.1128/mcb.01285-10openalex-snapshot

Heterochromatin Is Required for Normal Distribution of Neurospora crassa CenH3

inferredcites →https://doi.org/10.1128/mcb.8.2.754openalex-snapshot

Structural Organization and Functional Analysis of Centromeric DNA in the Fission Yeast Schizosaccharomyces pombe

inferredcites →https://doi.org/10.1146/annurev-micro-092611-150138openalex-snapshot

RNA Interference Pathways in Fungi: Mechanisms and Functions

inferredcites →https://doi.org/10.1146/annurev-phyto-102313-045933openalex-snapshot

Small RNAs: A New Paradigm in Plant-Microbe Interactions

inferredcites →https://doi.org/10.1186/1471-2164-12-288openalex-snapshot

Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

inferredcites →https://doi.org/10.1186/gb-2011-12-4-221openalex-snapshot

Vive la différence: biogenesis and evolution of microRNAs in plants and animals

inferredcites →https://doi.org/10.1186/s12864-015-1895-4openalex-snapshot

Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici)

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-015-0831-xopenalex-snapshot

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

inferredcites →https://doi.org/10.1186/s13059-016-0997-xopenalex-snapshot

Mash: fast genome and metagenome distance estimation using MinHash

inferredcites →https://doi.org/10.1186/s13100-015-0041-9openalex-snapshot

Repbase Update, a database of repetitive elements in eukaryotic genomes

inferredcites →https://doi.org/10.1242/jcs.061713openalex-snapshot

The role of small non-coding RNAs in genome stability and chromatin organization

inferredcites →https://doi.org/10.1261/rna.035279.112openalex-snapshot

ShortStack: Comprehensive annotation and quantification of small RNA genes

inferredcites →https://doi.org/10.12688/f1000research.7563.2openalex-snapshot

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

inferredcites →https://doi.org/10.1371/journal.pcbi.0010022openalex-snapshot

Combined Evidence Annotation of Transposable Elements in Genome Sequences

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.1371/journal.pone.0016526openalex-snapshot

Considering Transposable Element Diversification in De Novo Annotation Approaches

inferredcites →https://doi.org/10.1371/journal.ppat.1004329openalex-snapshot

The Ins and Outs of Rust Haustoria

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.2174/1389202915666141128002211openalex-snapshot

siRNA-directed DNA Methylation in Plants

inferredcites →https://doi.org/10.3389/fpls.2014.00759openalex-snapshot

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes

inferredcites →https://doi.org/10.3389/fpls.2016.00205openalex-snapshot

Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici

inferredcites →https://doi.org/10.4061/2011/716041openalex-snapshot

The Poplar-Poplar Rust Interaction: Insights from Genomics and Transcriptomics

inferredcites →https://doi.org/10.7717/peerj.4958openalex-snapshot

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/b978-0-12-819990-9.00042-1openalex-snapshot

Transposable Elements in Fungi: Coevolution With the Host Genome Shapes, Genome Architecture, Plasticity and Adaptation

inferred← citeshttps://doi.org/10.1016/j.micres.2020.126567openalex-snapshot

Effector Biology of Biotrophic Plant Fungal Pathogens: Current Advances and Future Prospects

inferred← citeshttps://doi.org/10.1016/j.ygeno.2022.110526openalex-snapshot

Small RNAs target native and cross-kingdom transcripts on both sides of the wheat stripe rust interaction

inferred← citeshttps://doi.org/10.1038/s41477-021-00971-5openalex-snapshot

Genomics accelerated isolation of a new stem rust avirulence gene–wheat resistance gene pair

inferred← citeshttps://doi.org/10.1093/g3journal/jkaa015openalex-snapshot

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

inferred← citeshttps://doi.org/10.1093/gbe/evaa071openalex-snapshot

Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat

inferred← citeshttps://doi.org/10.1242/jcs.237958openalex-snapshot

The plant–pathogen haustorial interface at a glance

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