PHI-base update: additions to the pathogen host interaction database

Winnenburg, Rainer; Urban, Martin; Beacham, Andrew M; Baldwin, Tyler; Holland, Sabrina M.; Lindeberg, Magdalen; Hansen, Hilde; Rawlings, Christopher J.; Hammond‐Kosack, K. E.; Köhler, Jacob

doi:10.1093/nar/gkm858

Cited by 146 publications

(157 citation statements)

References 12 publications

(17 reference statements)

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“…lack conserved domains (Dataset S1, Table S3). Most of the remaining lineage-specific genes have domains found in genes listed in the Pathogen-Host Interaction (PHI) database (16) or are effector-like small secreted cysteine-rich protein (SSCP) genes. SSCPs are frequently associated with host adaptation or specialization (17).…”

Section: Resultsmentioning

confidence: 99%

Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation

Xiao

Zheng

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

258

276

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Much remains unknown regarding speciation. Host-pathogen interactions are a major driving force for diversification, but the genomic basis for speciation and host shifting remains unclear. The fungal genus Metarhizium contains species ranging from specialists with very narrow host ranges to generalists that attack a wide range of insects. By genomic analyses of seven species, we demonstrated that generalists evolved from specialists via transitional species with intermediate host ranges and that this shift paralleled insect evolution. We found that specialization was associated with retention of sexuality and rapid evolution of existing protein sequences whereas generalization was associated with protein-family expansion, loss of genome-defense mechanisms, genome restructuring, horizontal gene transfer, and positive selection that accelerated after reinforcement of reproductive isolation. These results advance understanding of speciation and genomic signatures that underlie pathogen adaptation to hosts.peciation is a central component of biological diversification and is increasingly viewed as a continuum or process rather than an event. However, failure to identify transitional species has hindered progress in understanding genomic patterns of divergence along the speciation continuum (1). Plant or animal pathogenic fungi are genetically tractable models for the study of speciation due to their diverse lifestyles and the occurrence of sibling species that differ from each other principally in host specificity (2, 3). However, fundamental questions remain, including whether generalization or specialization to particular hosts is the ancestral condition, whether we can identify the existence of transitional forms, and what are the underlying molecular mechanisms driving speciation (4).We exploited the ascomycete genus Metarhizium, a radiating lineage of insect pathogens that are frequently used as biological insecticides (5, 6) and for genomic studies into the nature of adaptive differences by which novel pathogens emerge and form new species. Besides the previously sequenced Metarhizium robertsii (abbreviated as MAA) and Metarhizium acridum (MAC) (7), five new species were sequenced: Metarhizium album (MAM), Metarhizium majus (MAJ), Metarhizium guizhouense (MGU), Metarhizium brunneum (MBR), and Metarhizium anisopliae (MAN) (Dataset S1, Table S1). MAM is specific for hemipteran insects (8) whereas MAJ and MGU have intermediate host ranges as they are predominately associated with coleopteran insects but can also infect lepidopterans (9). Like MAA, MBR and MAN are generalists parasitizing a broad range of insects representing more than seven orders (10,11). Generalist species such as MAA and MBR can also colonize the roots of plants (12), consistent with increased phenotypic flexibility.Our analyses revealed that the evolutionary trajectory of Metarhizium spp. was from specialists via intermediate host range species to generalists that coincided with host insect diversification and availability. This host adaptati...

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Section: Resultsmentioning

confidence: 99%

Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation

Xiao

Zheng

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

258

276

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“…Members belonging to expanded Pfam families were exclusively encoded by core genes and comprised proteins containing the WSC domain (5 proteins), proteins with the PA14_2 (GLEYA) domain (1 protein), mucin (1 protein), peptidase_S8 (subtilisin) (1 protein), aspartyl protease (1 protein), and tyrosinase (1 protein) (Tables 1 and 2). Three of the proteins displayed sequence similarity to proteins in the pathogen-host interaction (PHI base) database of experimentally verified pathogenicity and virulence genes from fungi (20) (Table 1). …”

Section: Resultsmentioning

confidence: 99%

“…h Assigment of the biological or enzymatic function based on manual annotations. PHI, the protein displayed sequence similarity to proteins found in the pathogen-host interaction protein database (20); SSP, small (Ͻ300 amino acids) secreted proteins; K and I, the gene models were at least 2-fold upregulated in the RNA-Seq analysis in the pairwise comparisons of knob versus mycelium and infecting hyphae versus knob.…”

Section: Resultsmentioning

confidence: 99%

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Proteome of the Nematode-Trapping Cells of the Fungus Monacrosporium haptotylum

Andersson

Meerupati

Levander

et al. 2013

Appl Environ Microbiol

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Many nematophagous fungi use morphological structures called traps to capture nematodes by adhesion or mechanically. To better understand the cellular functions of adhesive traps, the trap cell proteome of the fungus Monacrosporium haptotylum was characterized. The trap of M. haptotylum consists of a unicellular structure called a knob that develops at the apex of a hypha. Proteins extracted from knobs and mycelia were analyzed using SDS-PAGE and liquid chromatography-tandem mass spectrometry (LC-MS-MS). The peptide sequences were matched against predicted gene models from the recently sequenced M. haptotylum genome. In total, 336 proteins were identified, with 54 expressed at significantly higher levels in the knobs than in the mycelia. The upregulated knob proteins included peptidases, small secreted proteins with unknown functions, and putative cell surface adhesins containing carbohydrate-binding domains, including the WSC domain. Phylogenetic analysis showed that all upregulated WSC domain proteins belonged to a large, expanded cluster of paralogs in M. haptotylum. Several peptidases and homologs of experimentally verified proteins in other pathogenic fungi were also upregulated in the knob proteome. Complementary profiling of gene expression at the transcriptome level showed poor correlation between the upregulation of knob proteins and their corresponding transcripts. We propose that the traps of M. haptotylum contain many of the proteins needed in the early stages of infection and that the trap cells can tightly control the translation and degradation of these proteins to minimize the cost of protein synthesis. N ematode-trapping fungi have the unique ability to capture and infect free-living nematodes (1). Given their potential use as biological control agents for plant-and animal-parasitic nematodes (2), there is much interest in studying their infection biology. To enter the parasitic stage, nematode-trapping fungi develop a unique morphological structure called traps. These traps develop from hyphal branches, either spontaneously or in response to signals from the environment, such as peptides or other compounds released by the host nematode (3). Molecular phylogeny studies have shown that the majority of nematode-trapping fungi belong to a monophyletic group in the order Orbiliales (Ascomycota). Within this clade, the trapping mechanisms have evolved along two major lineages, one leading to species with constricting rings and the other to species with adhesive traps, including three-dimensional networks, knobs, and branches (4-6).Despite large variation in their morphology, adhesive traps share a unique ultrastructure that clearly separates them from vegetative hyphae (3). One feature that is common to all traps is the presence of numerous cytosolic organelles called dense bodies. These organelles have catalase and D-amino acid oxidase activities, which indicates that they are peroxisome-like organelles (3). However, the function of these organelles is not yet fully understood. Another feature of th...

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“…pathoMIPer, Thiyagarajan et al, 2006;pyloriBASE, Ahmed et al 2007; VectorBase, Lawson et al, 2007;DengueInfo, Schreiber et al, 2007) or on plant pathogens (e.g. PhiBASE, Winnenburg et al, 2006). BOLD could serve as the universal starting point for species identification, which would convey users to refer to specialized databases (e.g.…”

Section: -3 Universality Of the Barcode Of Life Data System (Bold)mentioning

confidence: 99%