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Inference of Population Genetic Structure and High Linkage Disequilibrium Among Alternaria spp. Collected from Tomato and Potato Using Genotyping by Sequencing

https://doi.org/10.1101/827790
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Large-sporedAlternariapathogens in sectionPorridisentangled
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Shared ITS DNA substitutions in isolates of opposite mating type reveal a recombining history for three presumed asexual species in the filamentous ascomycete genus Alternaria
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Variability of Cuban and International Populations of Alternaria solani from Different Hosts and Localities: AFLP Genetic Analysis
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Population genetic analysis reveals cryptic sex in the phytopathogenic fungus Alternaria alternata
inferredcites →https://doi.org/10.1046/j.1364-3703.2003.00173.xopenalex-snapshot
Alternaria spp.: from general saprophyte to specific parasite
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Indices of multilocus linkage disequilibrium
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Analysis of Gene Diversity in Subdivided Populations
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Genetic Distance between Populations
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adegenet : a R package for the multivariate analysis of genetic markers
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The variant call format and VCFtools
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adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data
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Gametic Disequilibrium Measures: Proceed With Caution
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THE INTERACTION OF SELECTION AND LINKAGE. I. GENERAL CONSIDERATIONS; HETEROTIC MODELS
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MULTILOCUS STRUCTURE OF NATURAL POPULATIONS OF HORDEUM SPONTANEUM
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Origin and Domestication of the Fungal Wheat Pathogen Mycosphaerella graminicola via Sympatric Speciation
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Populations of Phytophthora rubi Show Little Differentiation and High Rates of Migration Among States in the Western United States
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Population Genetics of Fungal and Oomycete Effectors Involved in Gene-for-Gene Interactions
inferredcites →https://doi.org/10.1094/pdis-04-18-0703-pdnopenalex-snapshot
First Report of Early Blight Caused by Alternaria linariae on Potato in Algeria
inferredcites →https://doi.org/10.1094/pdis.2004.88.9.959openalex-snapshot
Genetic Diversity Among Alternaria solani Isolates from Potatoes in South Africa
inferredcites →https://doi.org/10.1094/phyto-06-18-0181-ropenalex-snapshot
Diversity and Virulence ofAlternariaspp. Causing Potato Early Blight and Brown Spot in Wisconsin
inferredcites →https://doi.org/10.1094/phyto-11-11-0321openalex-snapshot
Linkage Disequilibrium and Spatial Aggregation of Genotypes in Sexually Reproducing Populations of Erysiphe necator
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Best Practices for Population Genetic Analyses
inferredcites →https://doi.org/10.1094/phyto-65-880openalex-snapshot
A Stem Canker Disease of Tomato Caused by Alternaria alternata f. sp. lycopersici
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Production and Nature of a Host-Specific Toxin from Alternaria alternata f. sp. lycopersici
inferredcites →https://doi.org/10.1094/phyto-74-537openalex-snapshot
Pathogenicity ofAlternaria alternataon Potato in Israel
inferredcites →https://doi.org/10.1094/phyto-82-1343openalex-snapshot
Isozyme Variability inAlternaria solaniandA. alternata
inferredcites →https://doi.org/10.1094/phyto-99-6-0765openalex-snapshot
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A STANDARDIZED GENETIC DIFFERENTIATION MEASURE
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G ST and its relatives do not measure differentiation
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inferredcites →https://doi.org/10.1111/j.1365-3059.2004.01099.xopenalex-snapshot
New report of Alternaria alternata causing leaf blight of tomato in Pakistan
inferredcites →https://doi.org/10.1111/j.1439-0434.2010.01754.xopenalex-snapshot
Genetic Structure of the Population of Alternaria solani in Brazil
inferredcites →https://doi.org/10.1111/j.1558-5646.1960.tb03113.xopenalex-snapshot
THE EVOLUTIONARY DYNAMICS OF COMPLEX POLYMORPHISMS,,
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THE INTERPRETATION OF POPULATION STRUCTURE BY F-STATISTICS WITH SPECIAL REGARD TO SYSTEMS OF MATING
inferredcites →https://doi.org/10.1111/mpp.12214openalex-snapshot
Genotype‐by‐sequencing of the plant‐pathogenic fungi P yrenophora teres and S phaerulina musiva utilizing I on T orrent sequence technology
inferredcites →https://doi.org/10.1111/ppa.12275openalex-snapshot
High genotype diversity and lack of isolation by distance in the A lternaria solani populations from C hina
inferredcites →https://doi.org/10.1139/b95-383openalex-snapshot
The clonal dynamic in wild and agricultural plant–pathogen populations
inferredcites →https://doi.org/10.1146/annurev-phyto-080614-115913openalex-snapshot
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inferredcites →https://doi.org/10.1146/annurev.phyto.34.1.457openalex-snapshot
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inferredcites →https://doi.org/10.1186/s12864-015-1430-7openalex-snapshot
The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species
inferredcites →https://doi.org/10.1371/journal.pgen.0020190openalex-snapshot
Population Structure and Eigenanalysis
inferredcites →https://doi.org/10.1371/journal.pgen.1001189openalex-snapshot
Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola
inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
inferredcites →https://doi.org/10.1371/journal.pone.0062394openalex-snapshot
Habitat and Host Indicate Lineage Identity in Colletotrichum gloeosporioides s.l. from Wild and Agricultural Landscapes in North America
inferredcites →https://doi.org/10.1371/journal.pone.0085368openalex-snapshot
Population History and Pathways of Spread of the Plant Pathogen Phytophthora plurivora
inferredcites →https://doi.org/10.1371/journal.pone.0090346openalex-snapshot
TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
inferredcites →https://doi.org/10.1371/journal.pone.0106740openalex-snapshot
Recombination between Clonal Lineages of the Asexual Fungus Verticillium dahliae Detected by Genotyping by Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0143665openalex-snapshot
Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0165690openalex-snapshot
Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology
inferredcites →https://doi.org/10.1534/genetics.103.019638openalex-snapshot
Diverse Evolutionary Mechanisms Shape the Type III Effector Virulence Factor Repertoire in the Plant Pathogen Pseudomonas syringae
inferredcites →https://doi.org/10.1534/genetics.112.147710openalex-snapshot
Marker Density and Read Depth for Genotyping Populations Using Genotyping-by-Sequencing
inferredcites →https://doi.org/10.3389/fgene.2018.00123openalex-snapshot
Inferring Variation in Copy Number Using High Throughput Sequencing Data in R
inferredcites →https://doi.org/10.3389/fmicb.2017.00490openalex-snapshot
Population Structure of Sclerotinia subarctica and Sclerotinia sclerotiorum in England, Scotland and Norway
inferredcites →https://doi.org/10.3390/ijms18102019openalex-snapshot
Current Status of Early Blight Resistance in Tomato: An Update
inferredcites →https://doi.org/10.5197/j.2044-0588.2010.022.028openalex-snapshot
First report of Alternaria tomatophila and A. grandis causing early blight on tomato and potato in Brazil
inferredcites →https://doi.org/10.5860/choice.28-2137openalex-snapshot
The potato: evolution, biodiversity and genetic resources
inferredcites →https://doi.org/10.5962/p.414773openalex-snapshot
Alternaria themes and variations (244-286). Species on Solanaceae

What points at this work

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

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A pandemic clonal lineage of the wheat blast fungus
inferred← citeshttps://doi.org/10.1111/eva.13350openalex-snapshot
Whole‐genome sequencing elucidates the species‐wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani
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Distribution and Shared Pathogenicity of Small‐Spored Alternaria on Solanaceous Crops in Europe
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Distribution and Shared Pathogenicity of Small-Spored Alternaria on Solanaceous Crops in Europe
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