De novo Genome Assembly and Annotation of 12 Fungi Associated with Fruit Tree Decline Syndrome in ON, Canada.

Apple and stone fruit trees are vital components of Ontario's agricultural landscape. However, since 2016, these trees have been facing alarming mortality rates, exhibiting symptoms collectively referred to as Fruit Tree Decline (FTD) and Rapid Apple Decline (RAD). Despite its widespread occurrence, the exact cause of FTD and RAD remains elusive, with various pathogenic fungi and viruses implicated, along with abiotic stressors such as drought, winter injury and nutrient deficiency.

Characterisation of the genome and secretome of and .

Pethybr. & Laff. and Pethybr.

Correction: A target enrichment approach for enhanced recovery of Synchytrium endobioticum nuclear genome sequences.

[This corrects the article DOI: 10.1371/journal.pone.

Production of Ochratoxin A and Citrinin and the Expression of Their Biosynthetic Genes from in Liquid Culture.

is a fungal pathogen capable of producing two mycotoxins of concern, ochratoxin A (OTA) and citrinin (CIT). The production profile of these two mycotoxins is not well understood but could help mitigate co-contamination in the food supply. As such, the production of OTA and CIT from DAOMC 242724 was investigated under different growing conditions in liquid culture.

A target enrichment approach for enhanced recovery of Synchytrium endobioticum nuclear genome sequences.

Potato wart disease is caused by the obligate fungal pathogen Synchytrium endobioticum. DNA extraction from compost, purified spores and crude wart tissue derived from tuber galls of infected potatoes often results in low S. endobioticum DNA concentration or highly contaminated with DNA coming from other microorganisms and the potato host.

Genome Characterization and Development of Real-Time PCR Assays for and .

The stem and bulb nematode is a destructive nematode pest on many crops and is internationally quarantined in many countries, whereas , only known to infect a weed plant (), is an unregulated nematode species with no known economic importance. In this study, we used comparative genomics to identify multiple gene regions and developed novel real-time PCR assays for the detection of and . We sequenced the genomes of two mixed-stage nematode populations of and two mixed-stage nematode populations of .

Cytospora paraplurivora sp. nov. isolated from orchards with fruit tree decline syndrome in Ontario, Canada.

A new species of Cytospora was isolated from cankered wood of Prunus spp. during a survey of orchards exhibiting symptoms of fruit tree decline syndrome in southern Ontario, Canada. We found isolates that are morphologically similar to species in the Cytosporaceae family, which is characterized by single or labyrinthine locules, filamentous conidiophores or clavate to elongate obovoid asci and allantoid, hyaline conidia.

Whole genome sequencing and phylogenomic analysis show support for the splitting of genus .

The genus (nom. cons.) sensu lato (s.

Apicidin biosynthesis is linked to accessory chromosomes in Fusarium poae isolates.

Background: Fusarium head blight is a disease of global concern that reduces crop yields and renders grains unfit for consumption due to mycotoxin contamination. Fusarium poae is frequently associated with cereal crops showing symptoms of Fusarium head blight. While previous studies have shown F.

Development and evaluation of a target enrichment bait set for phylogenetic analysis of oomycetes.

Target enrichment is a term that encompasses multiple related approaches where desired genomic regions are captured by molecular baits, leaving behind redundant or non-target regions in the genome, followed by amplification and next-generation sequencing of those captured regions. A molecular bait set was developed based on 426 single-copy, oomycete-specific orthologs and 3 barcoding genes. The bait set was tested on 27 oomycete samples (belonging to the Saprolegniales, Albuginales, and Peronosporales) derived from live and herbarium specimens, as well as control samples of true fungi and plants.

Genome sequencing and comparison of five species to identify candidate genes for the detection of regulated species infecting wheat.

species cause diseases on grass hosts with some causing bunt diseases on wheat (). Two of the four species infecting wheat have restricted distributions globally and are subject to quarantine regulations to prevent their spread to new areas. causes Karnal bunt and is regulated by many countries while the non-regulated is morphologically similar and very closely related phylogenetically, but infects ryegrass () and not wheat.

Description and complete genome sequences of sp. nov., a non-symbiotic bacterium associated with legumes native to Canada.

Four bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soil of either (Hog Peanut) or (Showy Tick Trefoil) growing in Canada, were previously characterized and placed in a novel lineage within the genus . The taxonomic status of the novel strains was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated housekeeping gene sequences ( , , , and ) placed all novel strains in a highly supported lineage distinct from named species.

Description and complete genome sequence of sp. nov., harbouring photosystem and nitrogen-fixation genes.

A bacterial strain, designated 39S1MB, isolated from a root nodule of a soybean plant that had been inoculated with root-zone soil of (hog peanut) growing in Canada, was previously characterized and placed in a novel lineage within the genus . The taxonomic status of strain 39S1MB was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated protein-encoding gene sequences (, , , and ) placed 39S1MB in a lineage distinct from named species.

Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum.

Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported.

Nine draft genome sequences of ., including , and cf. pseudomolecules for the pitch canker pathogen , draft genome of and .

This genome announcement includes draft genomes from including , and cf. The draft genomes of and all three important eucalyptus pathogens, are presented. The insect associate is also described.

Complete Genome Sequence of Bradyrhizobium ottawaense OO99, an Efficient Nitrogen-Fixing Symbiont of Soybean.

We present the complete genome sequence of Bradyrhizobium ottawaense strain OO99, a nitrogen-fixing bacterium from root nodules of soybean. The genome consists of a single 8.6-Mb chromosome and includes a symbiosis island.

The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen.

Background: Chytridiomycota species (chytrids) belong to a basal lineage in the fungal kingdom. Inhabiting terrestrial and aquatic environments, most are free-living saprophytes but several species cause important diseases: e.g.

Wallemia peruviensis sp. nov., a new xerophilic fungus from an agricultural setting in South America.

We obtained four isolates of the xerophilic genus Wallemia from the rooftop of a house made of red brick and cement in an agronomic field planted with common beans and maize in Pachacamac, Lima, Peru. Bayesian phylogenetic analysis with rDNA gene sequences showed these Wallemia isolates form a distinct and strongly supported clade closely related to W. hederae.

Ochratoxin A production by Penicillium thymicola.

Ochratoxin A (OTA) is a mycotoxin produced by some Aspergillus and Penicillium species that grow on economically important agricultural crops and food products. OTA is classified as Group 2B carcinogen and is potently nephrotoxic, which is the basis for its regulation in some jurisdictions. Using high resolution mass spectroscopy, OTA and ochratoxin B (OTB) were detected in liquid culture extracts of Penicillium thymicola DAOMC 180753 isolated from Canadian cheddar cheese.

IMA Genome-F 6: Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723.

The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species.

Wickerhamomyces orientalis f.a., sp. nov.: an ascomycetous yeast species belonging to the Wickerhamomyces clade.

Five closely related yeast strains were isolated from soil in Kharg Island, Persian Gulf, Iran, and from fallen fruits in Galle, Sri Lanka, during separate projects. Morphologically, the strains produced white-coloured yeast colonies, with cells that were ovoid to ellipsoidal, making branched, true hyphae and pseudohyphae. Ascospore formation was not observed.

Draft Genome Sequence of Alternaria alternata ATCC 34957.

We report the draft genome sequence of Alternaria alternata ATCC 34957. This strain was previously reported to produce alternariol and alternariol monomethyl ether on weathered grain sorghum. The genome was sequenced with PacBio technology and assembled into 27 scaffolds with a total genome size of 33.

IMA Genome-F 5: Draft genome sequences of Ceratocystis eucalypticola, Chrysoporthe cubensis, C. deuterocubensis, Davidsoniella virescens, Fusarium temperatum,Graphilbum fragrans, Penicillium nordicum, and Thielaviopsis musarum.

The genomes of Ceratocystis eucalypticola, Chrysoporthe cubensis, Chrysoporthe deuterocubensis, Davidsoniella virescens, Fusarium temperatum, Graphilbum fragrans, Penicillium nordicum and Thielaviopsis musarum are presented in this genome announcement. These seven genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 28 Mb in the case of T.

Xerotolerant fungi in house dust: taxonomy of Spiromastix, Pseudospiromastix and Sigleria gen. nov. in Spiromastigaceae (Onygenales, Eurotiomycetes).

During a global investigation of fungi in house dust, we isolated six novel arthroconidial fungi. Phylogenies from combined analysis of nuc rDNA 18S, 28S and internal transcribed spacers sequences demonstrated that these fungi and two species preserved in culture collections represent undescribed species of Spiromastigaceae, Onygenales. Seven of the eight species lacked sexual states and only characters of asexual states and growth rates on different media could be used to characterize them.