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Dissecting the first phased dikaryotic genomes of the wheat rust pathogen Puccinia triticina reveals the mechanisms of somatic exchange in nature

https://doi.org/10.1101/705475
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What this work says

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

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Extraction of High Molecular Weight DNA from Fungal Rust Spores for Long Read Sequencing
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6 Mating Type in Basidiomycetes: Unipolar, Bipolar, and Tetrapolar Patterns of Sexuality
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Studies on the origin, spread, and evolution of an important group ofPuccinia recondita f. sp.tritici pathotypes in Australasia
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Multiallelic recognition: Nonself-dependent dimerization of the bE and bW homeodomain proteins in ustilago maydis
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Improved Prediction of Signal Peptides: SignalP 3.0
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Tracking wheat rust on a continental scale
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Somatic chromosome number in Puccinia recondita
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Induced mitotic crossing-over inUstilago maydis
inferredcites →https://doi.org/10.1017/s0953756298007631openalex-snapshot
Evidence for somatic hybridization in nature in Puccinia recondita f. sp. tritici, the leaf rust pathogen of wheat
inferredcites →https://doi.org/10.1038/hdy.2013.67openalex-snapshot
Evolution of uni- and bifactorial sexual compatibility systems in fungi
inferredcites →https://doi.org/10.1038/ncomms3673openalex-snapshot
High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus
inferredcites →https://doi.org/10.1038/nmeth.4035openalex-snapshot
Phased diploid genome assembly with single-molecule real-time sequencing
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De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
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Reassortment in segmented RNA viruses: mechanisms and outcomes
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Comparative genomic and transcriptional analyses of the carbohydrate-active enzymes and secretomes of phytopathogenic fungi reveal their significant roles during infection and development
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Stem rust of wheat in Australia
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Obligate biotrophy features unraveled by the genomic analysis of rust fungi
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GMAP: a genomic mapping and alignment program for mRNA and EST sequences
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Easyfig: a genome comparison visualizer
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InterProScan 5: genome-scale protein function classification
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
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Assemblytics: a web analytics tool for the detection of variants from an assembly
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Draft Genome of the Wheat Rust Pathogen ( Puccinia triticina) Unravels Genome-Wide Structural Variations during Evolution
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Inference of Population Structure Using Multilocus Genotype Data
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UniProt: the Universal Protein knowledgebase
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dbCAN: a web resource for automated carbohydrate-active enzyme annotation
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Pfam: the protein families database
inferredcites →https://doi.org/10.1093/nar/gkv1118openalex-snapshot
Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors
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tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
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Virulence and Molecular Characterization of Experimental Isolates of the Stripe Rust Pathogen (Puccinia striiformis) Indicate Somatic Recombination
inferredcites →https://doi.org/10.1094/phyto-99-12-1355openalex-snapshot
Fusion Body Formation, Germ Tube Anastomosis, and Nuclear Migration During the Germination of Urediniospores of the Wheat Leaf Rust Fungus, Puccinia triticina
inferredcites →https://doi.org/10.1094/phyto.1997.87.7.664openalex-snapshot
Sources and Patterns of Diversity in Plant-Pathogenic Fungi
inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot
Circos: An information aesthetic for comparative genomics
inferredcites →https://doi.org/10.1111/j.1365-3059.2008.01836.xopenalex-snapshot
Breeding cereals for rust resistance in Australia
inferredcites →https://doi.org/10.1111/j.1471-8286.2005.01155.xopenalex-snapshot
genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
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/10.1128/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/mmbr.62.1.55-70.1998openalex-snapshot
Molecular Genetics of Mating Recognition in Basidiomycete Fungi
inferredcites →https://doi.org/10.1146/annurev.mi.10.100156.002141openalex-snapshot
THE PARASEXUAL CYCLE IN FUNGI
inferredcites →https://doi.org/10.1186/1471-2105-12-124openalex-snapshot
Proteinortho: Detection of (Co-)orthologs in large-scale analysis
inferredcites →https://doi.org/10.1186/1471-2105-6-31openalex-snapshot
Automated generation of heuristics for biological sequence comparison
inferredcites →https://doi.org/10.1186/1471-2164-12-161openalex-snapshot
Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
inferredcites →https://doi.org/10.1186/1471-2164-14-270openalex-snapshot
Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. triticireveal polymorphic and haustorial expressed secreted proteins as candidate effectors
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
inferredcites →https://doi.org/10.1186/gb-2008-9-1-r7openalex-snapshot
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
inferredcites →https://doi.org/10.1186/s12859-018-2485-7openalex-snapshot
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
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/10.1534/g3.116.032797openalex-snapshot
Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci
inferredcites →https://doi.org/10.1534/genetics.114.164350openalex-snapshot
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
inferredcites →https://doi.org/10.3389/fgene.2013.00098openalex-snapshot
An overview of STRUCTURE: applications, parameter settings, and supporting software
inferredcites →https://doi.org/10.3389/fmicb.2018.00503openalex-snapshot
An Overview of the Function and Maintenance of Sexual Reproduction in Dikaryotic Fungi
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.2017.00148openalex-snapshot
Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia
inferredcites →https://doi.org/10.7717/peerj.281openalex-snapshot
Poppr : an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s10658-019-01903-yopenalex-snapshot
Sexual reproduction in populations of Austropuccinia psidii
inferred← citeshttps://doi.org/10.1038/s42003-021-01724-yopenalex-snapshot
Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi
inferred← citeshttps://doi.org/10.1186/s12915-023-01717-9openalex-snapshot
Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles
inferred← citeshttps://doi.org/10.24072/pcjournal.264openalex-snapshot
Evolution within a given virulence phenotype (pathotype) is driven by changes in aggressiveness: a case study of French wheat leaf rust populations
inferred← citeshttps://doi.org/10.3389/fmicb.2020.01188openalex-snapshot
Genome-Wide Identification of Effector Candidates With Conserved Motifs From the Wheat Leaf Rust Fungus Puccinia triticina
inferred← citeshttps://doi.org/10.6084/m9.figshare.26632006openalex-snapshot
Additional file 1 of Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles
inferred← citeshttps://doi.org/10.6084/m9.figshare.26632009openalex-snapshot
Additional file 2 of Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles
inferred← citeshttps://doi.org/10.6084/m9.figshare.26632012openalex-snapshot
Additional file 3 of Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles
inferred← citeshttps://doi.org/10.6084/m9.figshare.26632015openalex-snapshot
Additional file 4 of Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles
inferred← citeshttps://doi.org/10.6084/m9.figshare.26632018openalex-snapshot
Additional file 5 of Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles
inferred← citeshttps://doi.org/10.7554/elife.75917openalex-snapshot
Modeling the consequences of the dikaryotic life cycle of mushroom-forming fungi on genomic conflict
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