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The interspecific fungal hybrid Verticillium longisporum displays sub-genome-specific gene expression

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What this work says

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

inferredcites →https://doi.org/10.1002/bies.201300155openalex-snapshot

Sex or no sex: Evolutionary adaptation occurs regardless

inferredcites →https://doi.org/10.1002/yea.3242openalex-snapshot

Hybridization and emergence of virulence in opportunistic human yeast pathogens

inferredcites →https://doi.org/10.1007/978-1-4939-9173-0_14openalex-snapshot

BUSCO: Assessing Genome Assembly and Annotation Completeness

inferredcites →https://doi.org/10.1007/978-1-4939-9173-0_5openalex-snapshot

Whole-Genome Annotation with BRAKER

inferredcites →https://doi.org/10.1016/j.cels.2016.07.002openalex-snapshot

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

inferredcites →https://doi.org/10.1016/j.cub.2014.03.063openalex-snapshot

Chromosomal Rearrangements as a Major Mechanism in the Onset of Reproductive Isolation in Saccharomyces cerevisiae

inferredcites →https://doi.org/10.1016/j.mib.2016.04.005openalex-snapshot

Interspecific hybridization impacts host range and pathogenicity of filamentous microbes

inferredcites →https://doi.org/10.1016/j.pbi.2012.03.011openalex-snapshot

Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model

inferredcites →https://doi.org/10.1016/j.pbi.2014.05.001openalex-snapshot

Filamentous pathogen effector functions: of pathogens, hosts and microbiomes

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

EMBOSS: The European Molecular Biology Open Software Suite

inferredcites →https://doi.org/10.1038/hdy.2012.94openalex-snapshot

Homoeolog expression bias and expression level dominance in allopolyploid cotton

inferredcites →https://doi.org/10.1038/nature05706openalex-snapshot

Hybrid speciation

inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot

Full-length transcriptome assembly from RNA-Seq data without a reference genome

inferredcites →https://doi.org/10.1038/ncomms1954openalex-snapshot

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

inferredcites →https://doi.org/10.1038/ng.3485openalex-snapshot

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmicrobiol.2015.3openalex-snapshot

Speciation driven by hybridization and chromosomal plasticity in a wild yeast

inferredcites →https://doi.org/10.1038/nrg.2017.26openalex-snapshot

The evolutionary significance of polyploidy

inferredcites →https://doi.org/10.1038/nrmicro.2017.33openalex-snapshot

Ustilago maydis effectors and their impact on virulence

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/s41477-020-00799-5openalex-snapshot

Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins

inferredcites →https://doi.org/10.1038/s41559-018-0777-yopenalex-snapshot

Insights from genomes into the evolutionary importance and prevalence of hybridization in nature

inferredcites →https://doi.org/10.1038/s41587-019-0036-zopenalex-snapshot

SignalP 5.0 improves signal peptide predictions using deep neural networks

inferredcites →https://doi.org/10.1046/j.1365-294x.2001.01216.xopenalex-snapshot

The role of hybridization in evolution

inferredcites →https://doi.org/10.1073/pnas.0501102102openalex-snapshot

Modeling gene and genome duplications in eukaryotes

inferredcites →https://doi.org/10.1073/pnas.1119623109openalex-snapshot

Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing

inferredcites →https://doi.org/10.1073/pnas.1201403109openalex-snapshot

Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species

inferredcites →https://doi.org/10.1073/pnas.71.7.2848openalex-snapshot

On Some Principles Governing Molecular Evolution

inferredcites →https://doi.org/10.1093/bioinformatics/btaa179openalex-snapshot

Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

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/btu031openalex-snapshot

InterProScan 5: genome-scale protein function classification

inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

inferredcites →https://doi.org/10.1093/bioinformatics/btu393openalex-snapshot

circlize implements and enhances circular visualization in R

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

Minimap2: pairwise alignment for nucleotide sequences

inferredcites →https://doi.org/10.1093/femsyr/foaa040openalex-snapshot

Hybridization and the origin of new yeast lineages

inferredcites →https://doi.org/10.1093/gbe/evx072openalex-snapshot

Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species

inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot

PAML 4: Phylogenetic Analysis by Maximum Likelihood

inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

inferredcites →https://doi.org/10.1093/molbev/msx098openalex-snapshot

Loss of Heterozygosity Drives Adaptation in Hybrid Yeast

inferredcites →https://doi.org/10.1093/molbev/msx148openalex-snapshot

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

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/gks479openalex-snapshot

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

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/gky1085openalex-snapshot

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

inferredcites →https://doi.org/10.1093/nar/gky418openalex-snapshot

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

inferredcites →https://doi.org/10.1094/phyto-01-15-0030-fiopenalex-snapshot

Emergence and Spread of New Races of Wheat Stem Rust Fungus: Continued Threat to Food Security and Prospects of Genetic Control

inferredcites →https://doi.org/10.1094/phyto-05-17-0184-ropenalex-snapshot

The Emerging British Verticillium longisporum Population Consists of Aggressive Brassica Pathogens

inferredcites →https://doi.org/10.1094/phyto-08-15-0184-rvwopenalex-snapshot

The Role of Hybridization in the Evolution and Emergence of New Fungal Plant Pathogens

inferredcites →https://doi.org/10.1094/phyto-11-13-0315-iaopenalex-snapshot

VerticilliumSystematics and Evolution: How Confusion Impedes Verticillium Wilt Management and How to Resolve It

inferredcites →https://doi.org/10.1101/254797openalex-snapshot

The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000

inferredcites →https://doi.org/10.1101/gr.152660.112openalex-snapshot

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

inferredcites →https://doi.org/10.1101/gr.204974.116openalex-snapshot

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

inferredcites →https://doi.org/10.1101/gr.205948.116openalex-snapshot

Global deceleration of gene evolution following recent genome hybridizations in fungi

inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation

inferredcites →https://doi.org/10.1111/1462-2920.13801openalex-snapshot

A distinct and genetically diverse lineage of the hybrid fungal pathogen Verticillium longisporum population causes stem striping in British oilseed rape

inferredcites →https://doi.org/10.1111/1462-2920.14037openalex-snapshot

Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss

inferredcites →https://doi.org/10.1111/j.1469-8137.2012.04365.xopenalex-snapshot

Homoeolog expression bias and expression level dominance in allopolyploids

inferredcites →https://doi.org/10.1111/mec.15168openalex-snapshot

Dynamic virulence‐related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation

inferredcites →https://doi.org/10.1111/mpp.12350openalex-snapshot

Verticillium longisporum , the invisible threat to oilseed rape and other brassicaceous plant hosts

inferredcites →https://doi.org/10.1111/mpp.12520openalex-snapshot

Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts

inferredcites →https://doi.org/10.1111/mpp.12628openalex-snapshot

Plant pathogen effector proteins as manipulators of host microbiomes?

inferredcites →https://doi.org/10.1126/science.1169766openalex-snapshot

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation

inferredcites →https://doi.org/10.1126/science.1188021openalex-snapshot

A Draft Sequence of the Neandertal Genome

inferredcites →https://doi.org/10.1126/science.1193440openalex-snapshot

A Test of the Snowball Theory for the Rate of Evolution of Hybrid Incompatibilities

inferredcites →https://doi.org/10.1126/science.15739260openalex-snapshot

The Significance of Responses of the Genome to Challenge

inferredcites →https://doi.org/10.1126/science.290.5494.1151openalex-snapshot

The Evolutionary Fate and Consequences of Duplicate Genes

inferredcites →https://doi.org/10.1126/science.aal3327openalex-snapshot

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

inferredcites →https://doi.org/10.1128/mbio.00936-15openalex-snapshot

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

inferredcites →https://doi.org/10.1146/annurev-arplant-043014-114623openalex-snapshot

Fungal Effectors and Plant Susceptibility

inferredcites →https://doi.org/10.1146/annurev-genet-110410-132514openalex-snapshot

The Genetics of Hybrid Incompatibilities

inferredcites →https://doi.org/10.1146/annurev-phyto-080614-120114openalex-snapshot

Understanding Plant Immunity as a Surveillance System to Detect Invasion

inferredcites →https://doi.org/10.1186/1471-2105-12-116openalex-snapshot

Ultra-fast sequence clustering from similarity networks with SiLiX

inferredcites →https://doi.org/10.1186/1741-7007-5-31openalex-snapshot

Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis

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-2013-14-4-r36openalex-snapshot

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

inferredcites →https://doi.org/10.1186/s12864-019-6222-zopenalex-snapshot

Effects of parental genetic divergence on gene expression patterns in interspecific hybrids of Camellia

inferredcites →https://doi.org/10.1186/s12915-020-00776-6openalex-snapshot

Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

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/10.1371/journal.pbio.1002220openalex-snapshot

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

inferredcites →https://doi.org/10.1371/journal.pbio.2002128openalex-snapshot

Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch

inferredcites →https://doi.org/10.1371/journal.pgen.1004180openalex-snapshot

An Interspecific Fungal Hybrid Reveals Cross-Kingdom Rules for Allopolyploid Gene Expression Patterns

inferredcites →https://doi.org/10.1371/journal.pgen.1005626openalex-snapshot

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis

inferredcites →https://doi.org/10.1371/journal.pgen.1006404openalex-snapshot

Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species

inferredcites →https://doi.org/10.1371/journal.pgen.1007613openalex-snapshot

In search of the Goldilocks zone for hybrid speciation

inferredcites →https://doi.org/10.1371/journal.pgen.1008404openalex-snapshot

Eukaryote hybrid genomes

inferredcites →https://doi.org/10.1371/journal.pone.0018260openalex-snapshot

The Ascomycete Verticillium longisporum Is a Hybrid and a Plant Pathogen with an Expanded Host Range

inferredcites →https://doi.org/10.1371/journal.pone.0028341openalex-snapshot

Phylogenetics and Taxonomy of the Fungal Vascular Wilt Pathogen Verticillium, with the Descriptions of Five New Species

inferredcites →https://doi.org/10.1371/journal.ppat.1002137openalex-snapshot

Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens

inferredcites →https://doi.org/10.1534/g3.111.000745openalex-snapshot

Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization

inferredcites →https://doi.org/10.3389/fgene.2019.00383openalex-snapshot

Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin

inferredcites →https://doi.org/10.3389/fgene.2020.00404openalex-snapshot

Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization

inferredcites →https://doi.org/10.3389/fmicb.2016.00429openalex-snapshot

Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display

inferredcites →https://doi.org/10.3389/fpls.2018.00049openalex-snapshot

Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen

inferredcites →https://doi.org/10.7554/elife.62208openalex-snapshot

A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen

inferredcites →https://doi.org/10.7717/peerj-cs.118openalex-snapshot

VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41477-020-00799-5openalex-snapshot

Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins

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