The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens

Annual Review of Phytopathology, Journal Year: 2018, Volume and Issue: 56(1), P. 21 - 40

Published: May 16, 2018

Filamentous pathogens, including fungi and oomycetes, pose major threats to global food security. Crop pathogens cause damage by secreting effectors that manipulate the host pathogen's advantage. Genes encoding such are among most rapidly evolving genes in pathogen genomes. Here, we review how characteristics of emergence, function, regulation effector tightly linked genomic compartments where these located The presence repetitive elements is associated with elevated rates point mutations sequence rearrangements a impact on diversification. expression many converges an epigenetic control mediated elements. Population genomics analyses showed show high turnover at loci display mosaic presence-absence polymorphism strains. We conclude effective containment strategies require thorough understanding genome biology potential for rapid adaptation.

Language: Английский

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Colletotrichum: species complexes, lifestyle, and peculiarities of some sources of genetic variability

Applied Microbiology and Biotechnology, Journal Year: 2020, Volume and Issue: 104(5), P. 1891 - 1904

Published: Jan. 14, 2020

Language: Английский

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Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

PLoS Genetics, Journal Year: 2018, Volume and Issue: 14(10), P. e1007467 - e1007467

Published: Oct. 24, 2018

Structural features of genomes, including the three-dimensional arrangement DNA in nucleus, are increasingly seen as key contributors to regulation gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited a handful model species. This narrow focus limits our ability draw general conclusions about ways which structures encoded, integrate information from data address broader gamut biological questions. Here, we generate complete gapless sequence for filamentous fungus, Epichloë festucae. We use Hi-C examine genome, RNA-seq investigate contributes suite transcriptional changes needed maintain symbiotic relationships with grass host. Our results reveal very repeat-rich blocks discrete boundaries interspersed by gene-rich sequences that almost repeat-free. In contrast other species reported date, is anchored these repeat blocks, act isolate neighbouring regions. Genes differentially expressed planta enriched near suggesting their orientation partly encodes regulates relationship formed this organism.

Language: Английский

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Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: May 11, 2018

Xenovulene A is a complex fungal meroterpenoid, produced by the organism hitherto known as Acremonium strictum IMI 501407, for which limited biosynthetic evidence exists. Here, we generate draft genome and show that producing previously unknown should be renamed Sarocladium schorii. gene cluster discovered bears resemblance to those involved in biosynthesis of tropolones, with additional genes function. Heterologous reconstruction entire pathway Aspergillus oryzae allows chemical steps dissected. The shows very similarity other meroterpenoids. features: initial formation tropolone intermediates; likely involvement hetero Diels-Alder enzyme; terpene cyclase no significant sequence homology any two enzymes catalysing oxidative-ring contractions.

Language: Английский

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Nonproteinaceous effectors: the terra incognita of plant–fungal interactions

New Phytologist, Journal Year: 2019, Volume and Issue: 223(2), P. 590 - 596

Published: March 9, 2019

Summary Molecular plant–fungal interaction studies have mainly focused on small secreted protein effectors. However, accumulating evidence shows that numerous fungal secondary metabolites are produced at all stages of plant colonization, especially during early asymptomatic/biotrophic phases. The discovery RNA s targeting transcripts has expanded the repertoire nonproteinaceous effectors even further. challenge now is to develop specific functional methods fully understand biological roles these Studies extracellular vesicles also needed because they could be universal carriers kinds With this review, we aim stimulate effector research field move from descriptive studies, which should bring a paradigm shift in interactions.

Language: Английский

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Giant Transposons in Eukaryotes: Is Bigger Better?

Genome Biology and Evolution, Journal Year: 2019, Volume and Issue: 11(3), P. 906 - 918

Published: Feb. 22, 2019

Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations shapes genome structure function a multitude ways. In traditional classification systems, TEs often being depicted simplistic ways, based primarily on key enzymes required for transposition, such as transposases/recombinases reverse transcriptases. Recent progress whole-genome sequencing long-read assembly, combined expansion familiar range model organisms, resulted identification unprecedentedly long transposable units spanning dozens or even hundreds kilobases, initially prokaryotic more recently eukaryotic systems. Here, we focus oversized TEs, including retrotransposons DNA transposons, outline complex combinatorial nature closely intertwined relationship viruses, discuss potential participating transfer stretches eukaryotes.

Language: Английский

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

Microbiological Research, Journal Year: 2020, Volume and Issue: 241, P. 126567 - 126567

Published: Aug. 23, 2020

Language: Английский

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Construction of a chromosome‐level genome and variation map for the Pacific oyster Crassostrea gigas

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(5), P. 1670 - 1685

Published: March 3, 2021

Abstract The Pacific oyster ( Crassostrea gigas ) is a widely distributed marine bivalve of great ecological and economic importance. In this study, we provide high‐quality chromosome‐level genome assembled using Bioscience long reads Hi‐C‐based linkage‐map‐based scaffolding technologies high‐resolution variation map constructed large‐scale resequencing analysis. 586.8 Mb consists 10 pseudochromosome sequences ranging from 38.6 to 78.9 Mb, containing 301 contigs with an N50 size 3.1 Mb. A total 30,078 protein‐coding genes were predicted, which 22,757 (75.7%) high‐reliability annotations supported by homologous match curated protein in the SWISS‐PROT database or transcript expression. Although medium level repeat components (57.2%) was detected, genomic content segmental duplications reached 26.2%, highest among reported genomes. By whole analysis 495 oysters, comprehensive built, comprised 4.78 million single nucleotide polymorphisms, 0.60 short insertions deletions, 49,333 copy number regions. structural variations can lead average interindividual divergence 0.21, indicating their crucial role shaping diversity. large amount mosaic elements, small variations, indicate that diploid organism extremely high complexity at intra‐ level. maps improve our understanding diversity enrich resources for molecular evolution, comparative genomics, genetic research.

Language: Английский

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Fast characterization of segmental duplications in genome assemblies

Bioinformatics, Journal Year: 2018, Volume and Issue: 34(17), P. i706 - i714

Published: July 7, 2018

Segmental duplications (SDs) or low-copy repeats, are segments of DNA > 1 Kbp with high sequence identity that copied to other regions the genome. SDs among most important sources evolution, a common cause genomic structural variation and several associated diseases origin including schizophrenia autism. Despite their functional importance, present one major hurdles for de novo genome assembly due ambiguity they in building traversing both state-of-the-art overlap-layout-consensus Bruijn graphs. This causes SD be misassembled, collapsed into unique representation, completely missing from assembled reference genomes various organisms. In turn, this incorrect information limits our ability fully understand evolution architecture genomes. essential need accurately characterize assemblies, there has been only tool was developed purpose, called Whole-Genome Assembly Comparison (WGAC); its primary goal is detection. WGAC comprised steps employ different tools custom scripts, which makes strategy difficult time consuming use. Thus still algorithms within-assembly quickly, accurately, user friendly manner.Here we introduce SEgmental Duplication Evaluation Framework (SEDEF) rapidly detect through sophisticated filtering strategies based on Jaccard similarity local chaining. We show SEDEF detects while maintaining substantial speed up over translates practical run times minutes instead weeks. Notably, algorithm captures 25% 'pairwise error' between segments, whereas previous studies focused 10%, allowing us more deeply track evolutionary history genome.SEDEF available at https://github.com/vpc-ccg/sedef.

Language: Английский

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

Molecular Plant Pathology, Journal Year: 2019, Volume and Issue: 20(9), P. 1279 - 1297

Published: July 30, 2019

Summary Fungal plant pathogens secrete effector proteins and metabolites to cause disease. Additionally, some species transfer small RNAs (sRNAs) into cells silence host mRNAs through complementary base pairing suppress immunity. The fungus Sclerotinia sclerotiorum infects over 600 species, but little is known about the molecular processes that govern interactions with its many hosts. In particular, evidence for production of sRNAs by S. during infection lacking. We sequenced produced in vitro two Arabidopsis thaliana Phaseolus vulgaris . found produces at least 374 distinct highly abundant infection, mostly originating from repeat‐rich plastic genomic regions. predicted targets these A. genes were significantly more down‐regulated than rest genome. Predicted enriched functional domains associated immunity strongly quantitative disease resistance a genome‐wide association study (GWAS) Mutants sRNA target SERK2 SNAK2 susceptible wild‐type, suggesting may contribute silencing immune components plants. prediction fungal genomes can be combined other global approaches, such as GWAS, assist identification involved resistance.

Language: Английский

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