Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Nucleic Acids Research, Год журнала: 2017, Номер 46(D1), С. D802 - D808

Опубликована: Окт. 24, 2017

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources vertebrate genomics developed in project (http://www.ensembl.org). Together, two provide a consistent set of programmatic and interactive interfaces to rich range including genome sequence, gene models, transcript genetic variation, comparative analysis. This paper provides update previous publications about resource, with focus on recent developments expansions. These include incorporation almost 20 000 additional sequences over 35 tracks RNA-Seq data, which have been aligned genomic sequence made available visualization. Other advances since 2015 release database Resource Description Framework (RDF) format, large increase community-derived curation, new high-performance protein search, cross-references, improved annotation non-protein-coding genes, launch pre-release archival sites. Collectively, these changes are part continuing response increasing quantity publicly-available consequent need archive, integrate, annotate disseminate using automated, scalable methods.

Язык: Английский

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Grey mould of strawberry, a devastating disease caused by the ubiquitous necrotrophic fungal pathogen Botrytis cinerea

Molecular Plant Pathology, Год журнала: 2019, Номер 20(6), С. 877 - 892

Опубликована: Апрель 4, 2019

The fungal pathogen Botrytis cinerea causes grey mould, a commercially damaging disease of strawberry. This affects fruit in the field, storage, transport and market. presence mould is most common reason for rejection by growers, shippers consumers, leading to significant economic losses. Here, we review biology epidemiology pathogen, mechanisms infection genetics host plant resistance. development affected environmental genetic factors; however, little known about how B. strawberry interact at molecular level. Despite intensive efforts, breeding resistance has not been successful, underlying tolerance are poorly understood under-investigated. Current control strategies against include pre- postharvest fungicides, yet they generally ineffective expensive. In this review, examine available research on horticultural management, chemical biological field discuss their relevance integrative management. Additionally, identify propose approaches increasing tapping into natural variation manipulating factors via engineering genome editing.

Язык: Английский

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MYC2 Orchestrates a Hierarchical Transcriptional Cascade That Regulates Jasmonate-Mediated Plant Immunity in Tomato

The Plant Cell, Год журнала: 2017, Номер 29(8), С. 1883 - 1906

Опубликована: Июль 21, 2017

The hormone jasmonate (JA), which functions in plant immunity, regulates resistance to pathogen infection and insect attack through triggering genome-wide transcriptional reprogramming plants. We show that the basic helix-loop-helix transcription factor (TF) MYC2 tomato (Solanum lycopersicum) acts downstream of JA receptor orchestrate JA-mediated activation both wounding responses. Using chromatin immunoprecipitation sequencing (ChIP-seq) coupled with RNA (RNA-seq) assays, we identified 655 MYC2-targeted JA-responsive genes. These genes are highly enriched Gene Ontology categories related TFs early response JA, indicating at a high hierarchical level regulate gene transcription. also group (MTFs) may directly JA-induced late defense Our findings suggest its MTFs form cascade during immunity initiates amplifies output. As proof concept, showed necrotrophic Botrytis cinerea, MTF JA2-Like module preferentially wounding-responsive genes, whereas ETHYLENE RESPONSE FACTOR.C3 pathogen-responsive

Язык: Английский

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The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens

Annual Review of Phytopathology, Год журнала: 2018, Номер 56(1), С. 21 - 40

Опубликована: Май 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.

Язык: Английский

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The Complete Genome Sequence of the Phytopathogenic Fungus Sclerotinia sclerotiorum Reveals Insights into the Genome Architecture of Broad Host Range Pathogens

Genome Biology and Evolution, Год журнала: 2017, Номер 9(3), С. 593 - 618

Опубликована: Фев. 15, 2017

Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many destructive pathogens that only exhibit single or very few hosts. Many plant "two-speed" genome. So described because their genomes contain alternating gene rich, repeat sparse and poor, repeat-rich regions. In fungi, the regions may be subjected to process termed repeat-induced point mutation (RIP). Both activity RIP are thought play significant role in evolution of secreted virulence proteins, effectors. We present complete genome sequence S. generated using Single Molecule Real-Time Sequencing technology highly accurate annotations produced an extensive RNA sequencing data set. identified 70 effector candidates have highlighted planta expression profiles. Furthermore, we characterized architecture comparison genomes. show there association between positions proteins high index but did not detect correlation protein proportion GC content. Neither negative CDS content across conclude exhibits subtle signatures enhanced specific genomic compartments as result transposition activity. However, these observable at whole-genome scale.

Язык: Английский

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AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 27, 2023

Abstract Adapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Here, we used AlphaFold-Multimer (AFM) to screen 1879 SSPs seven tomato for interacting six defence-related hydrolases tomato. This 11,274 protein pairs identified 15 non-annotated that are predicted obstruct the active site chitinases and proteases an intrinsic fold. Four were experimentally verified be inhibitors pathogenesis-related subtilase P69B, including extracellular protein-36 (Ecp36) secreted-into-xylem-15 (Six15) fungal Cladosporium fulvum Fusarium oxysporum , respectively. Together a P69B inhibitor bacterial pathogen Xanthomonas perforans Kazal-like oomycete Phytophthora infestans emerges as effector hub targeted by different kingdoms, consistent diversification orthologs paralogs. study demonstrates power artificial intelligence predict cross-kingdom interactions at plant-pathogen interface.

Язык: Английский

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Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

Science, Год журнала: 2024, Номер 384(6694)

Опубликована: Апрель 25, 2024

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to broad (generalists). Two general paradigms have been proposed explain this variation: (i) trade-offs between performance efficiency and breadth (ii) the joint influence of extrinsic (environmental) intrinsic (genomic) factors. We assembled genomic, metabolic, data nearly all known species ancient fungal subphylum Saccharomycotina (1154 yeast strains 1051 species), grown 24 different environmental conditions, examine evolution. found that large differences carbon utilization traits yeasts stem genes encoding specific metabolic pathways, but we limited evidence for trade-offs. These comprehensive argue factors shape microbes.

Язык: Английский

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Advances in the molecular mechanism of grapevine resistance to fungal diseases

Molecular Horticulture, Год журнала: 2025, Номер 5(1)

Опубликована: Янв. 2, 2025

Abstract Grapevine is an important economic fruit tree worldwide, but grape production has been plagued by a vast number of fungal diseases, which affect vigor and the quality yield berries. To seek remedies for such issues, researchers have always committed to conventional biotechnological breeding. In recent years, increasing progress made in elucidating molecular mechanisms grape–pathogenic fungi interactions resistance regulation. Here, we summarize current knowledge on basis grapevine including effector-mediated susceptibility resistance, resistant regulatory networks grapevine, innovative approaches genetic transformation, strategies improve resistance. Understanding exploring accurately regulating diseases.

Язык: Английский

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Mechanisms of Broad Host Range Necrotrophic Pathogenesis in Sclerotinia sclerotiorum

Phytopathology, Год журнала: 2018, Номер 108(10), С. 1128 - 1140

Опубликована: Июль 26, 2018

Among necrotrophic fungi, Sclerotinia sclerotiorum is remarkable for its extremely broad host range and aggressive tissue colonization. With full genome sequencing, transcriptomic analyses the increasing pace of functional gene characterization, factors underlying basis this pathogenesis are now being elucidated at a greater pace. these, genes have been characterized that required infection via compound appressoria in addition to associated with colonization regulate oxalic acid (OA) production OA catabolism. Moreover, virulence-related secretory proteins identified, among which candidates manipulating activities apoplastically cytoplasmically. Coupled these mechanistic studies, cytological observations process blurred heretofore clear-cut biotroph versus necrotroph boundary. In review, we reexamine cytology S. put more recent molecular genomic data into context cytology. We propose two-phase model pathogen first evades, counteracts subverts basal defense reactions prior killing degrading cells. Spatially, may achieve compatibility factors/effectors appressoria, bulbous subcuticular hyphae, primary invasive hyphae. By examining nuances interaction, hope illuminate new classes as targets improve our understanding pathogens provide corresponding resistance.

Язык: Английский

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A mobile pathogenicity chromosome in Fusarium oxysporum for infection of multiple cucurbit species

Scientific Reports, Год журнала: 2017, Номер 7(1)

Опубликована: Авг. 16, 2017

Abstract The genome of Fusarium oxysporum (Fo) consists a set eleven ‘core’ chromosomes, shared by most strains and responsible for housekeeping, one or several accessory chromosomes. We sequenced strain Fo f.sp. radicis - cucumerinum (Forc) using PacBio SMRT sequencing. All but the core chromosomes were assembled into single contigs, chromosome that shows all hallmarks pathogenicity comprised two contigs. A central part this contains identified candidate effector genes, including homologs SIX6 , SIX9 SIX11 SIX 13 . show 6 contributes to virulence Forc. Through horizontal transfer (HCT) non-pathogenic strain, we also containing gene is indeed cucurbit infection. Conversely, complete loss was observed in Forc016 lost chromosome. conclude non-wilt-inducing pathogen relies on proteins successful infection Forc information necessary causing root rot cucurbits. Three out nine HCT investigated have undergone large-scale alterations, reflecting remarkable plasticity genomes.

Язык: Английский

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