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. musarum to 45 Mb for Fusarium temperatum. These genomes include the first reports of genomes for the genera Davidsoniella, Graphilbum and Thielaviopsis. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.
This genome announcement includes draft genomes from
Claviceps purpurea s.lat.,
including
C. arundinis
,
C. humidiphila
and
C.
cf.
spartinae
.
The draft genomes of
Davidsoniella eucalypti, Quambalaria eucalypti
and
Teratosphaeria destructans,
all three important eucalyptus pathogens, are presented. The insect associate
Grosmannia galeiformis
is also described. The pine pathogen genome of
Fusarium circinatum
has been assembled into pseudomolecules, based on additional sequence data and by harnessing the known synteny within the
Fusarium fujikuroi
species complex. This new assembly of the
F. circinatum
genome provides 12 pseudomolecules that correspond to the haploid chromosome number of
F. circinatum
. These are comparable to other chromosomal assemblies within the FFSC and will enable more robust genomic comparisons within this species complex.
Using a heat-treatment method, two genera of heat-resistant and xerotolerant basidiomycetes were isolated from soil samples. These two genera, Basidioascus and Geminibasidium gen. nov., are morphologically similar and phylogenetically related. The genus Basidioascus originally was described as an ascomycete, but the structures originally interpreted as single-spored asci appear to represent basidiospores. Morphologically both genera are characterized by the lack of a fruiting body, conspicuously granular and deciduous basidia with a unique basal lateral projection and apparently double-walled basidiospores. The basidia, rather than the basidiospores, are forcibly discharged in Basidioascus species but not in Geminibasidium species. In Geminibasidium species a putative basidium arises from a primary cell. These are novel forms of basidia ontogenesis previously unseen in basidiomycetes. The rDNA (SSU + 5.8S + LSU) Bayesian phylogenetic analysis suggests that these fungi are distantly related to Wallemia, another xerotolerant basidiomycete genus commonly found in indoor air dust, dried foods and natural hypersaline environments. Given the physiological similarity and phylogenetic relationships, Basidioascus and Geminibasidium are classified in a new order, Geminibasidiales, and are taxonomically assigned to the class Wallemiomycetes. Based on morphological observations and molecular phylogeny of the internal transcribed spacer (ITS), two species of Basidioascus (B. undulatus, B. magus sp. nov.) and two species of Geminibasidium (G. donsium sp. nov., G. hirsutum sp. nov.) are described. A key to these species is provided using micromorphological and cultural characters.
Wallemia sebi is a xerophilic food- and air-borne fungus. The name has been used for strains that prevail in cold, temperate and tropical climates. In this study, multi-locus phylogenetic analyses, using the internal transcribed spacer (ITS) regions, DNA replication licensing factor (MCM7), pre-rRNA processing protein (TSR1), RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2) and a new marker 3´-phosphoadenosine-5´-phosphatase (HAL2), confirmed the previous hypothesis that W. sebi presents a complex of at least four species. Here, we confirm and apply the phylogenetic analyses based species hypotheses from a companion study to guide phenotypic assessment of W. sebi like strains from a wide range of substrates, climates and continents allowed the recognition of W. sebi sensu stricto and three new species described as W. mellicola, W. Canadensis, and W. tropicalis. The species differ in their conidial size, xerotolerance, halotolerance, chaotolerance, growth temperature regimes, extracellular enzyme activity profiles, and secondary metabolite patterns. A key to all currently accepted Wallemia species is provided that allow their identification on the basis of physiological, micromorphological and culture characters.
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. Essential purine pathway genes were found uniquely absent in
S. endobioticum
, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids
Batrachochytrium dendrobatidis
and
S. endobioticum
contained the largest amounts of repeats, and we identified
S. endobioticum
specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in
S. endobioticum
, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.
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