FunSecKB2: a fungal protein subcellular location knowledgebase

Meinken, John; Asch, David K.; <, Kofi A. Neizer-Ashun; <, Guang-Hwa Chang; Cooper, Chester R.; Min, Xiang Jia

doi:10.5376/cmb.2014.04.0007

Cited by 30 publications

(31 citation statements)

References 41 publications

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“…The secretome of a pathogen includes extracellular secreted proteins that are deployed to the host–pathogen interface during infection and includes important virulence factors such as effector proteins for manipulation of host cell dynamics and cell wall degrading enzymes. A highly stringent pipeline for secretome prediction in fungi, as described in FunSecKB2 [ 81 ] ( Fig 3 ), was implemented to predict a refined secretome in C . truncatum (1,257 proteins) that represented 9.16% of the total proteome.…”

Section: Resultsmentioning

confidence: 99%

“…However, some of the known effectors have homologues in related fungi as well as functional domains [ 94 – 96 ], though fungal effector proteins do not share a conserved host targeting signal like RxLR motifs of Oomycetes. A stringent strategy based on the tools described for fungal secretome prediction [ 81 ] was used in this study for the prediction of proteins that are highly likely to be secreted in C . truncatum as well as in other fungi.…”

Section: Discussionmentioning

confidence: 99%

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Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum

Rao

Nandineni

2017

PLoS ONE

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Colletotrichum truncatum, a major fungal phytopathogen, causes the anthracnose disease on an economically important spice crop chilli (Capsicum annuum), resulting in huge economic losses in tropical and sub-tropical countries. It follows a subcuticular intramural infection strategy on chilli with a short, asymptomatic, endophytic phase, which contrasts with the intracellular hemibiotrophic lifestyle adopted by most of the Colletotrichum species. However, little is known about the molecular determinants and the mechanism of pathogenicity in this fungus. A high quality whole genome sequence and gene annotation based on transcriptome data of an Indian isolate of C. truncatum from chilli has been obtained. Analysis of the genome sequence revealed a rich repertoire of pathogenicity genes in C. truncatum encoding secreted proteins, effectors, plant cell wall degrading enzymes, secondary metabolism associated proteins, with potential roles in the host-specific infection strategy, placing it next only to the Fusarium species. The size of genome assembly, number of predicted genes and some of the functional categories were similar to other sequenced Colletotrichum species. The comparative genomic analyses with other species and related fungi identified some unique genes and certain highly expanded gene families of CAZymes, proteases and secondary metabolism associated genes in the genome of C. truncatum. The draft genome assembly and functional annotation of potential pathogenicity genes of C. truncatum provide an important genomic resource for understanding the biology and lifestyle of this important phytopathogen and will pave the way for designing efficient disease control regimens.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum

Rao

Nandineni

2017

PLoS ONE

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“…OrfPredictor software predicted the ESTs of the transcripts with differential up-regulated genes during infection and translated the ESTs into amino acid sequences (Min et al, 2005). The predicted proteins as queries hit secreted proteins in Fungal Secretomes of FunSecKB2 database with Blastp at value 1E-5 (Meinken et al, 2014). The same predicted proteins were also analyzed in the EffectorP 2.0 beta database for predicting the candidate effector genes (Dodds et al, 2016).…”

Section: Candidate Effector and Secretory Genes Analysismentioning

confidence: 99%

Distinctive Gene Expression Profiles and Effectors Consistent With Host Specificity in Two Formae Speciales of Marssonina brunnea

Ren

Yan

et al. 2020

Front. Microbiol.

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The knowledge on the host specificity of a pathogen underlying an interaction is becoming an urgent necessity for global warming. In this study, the gene expression profiles and the roles of effectors in host specificity were integrally characterized with two formae speciales, multigermtubi and monogermtubi, of a hemibiotrophic pathogen Marssonina brunnea when they were infecting respective susceptible poplar hosts. With a functional genome comparison referring to a de novo transcriptome of M. brunnea and Pathogen-Host Interaction database functional annotations, the multigermtubi strain showed abundant and significant differentially expressed unigenes (DEGs) (more than 40%) in colonizing the initial invasion stage and in the necrotrophic stage. The monogermtubi strain induced less than 10% of DEGs in the initial invasion stage but which abruptly increased to more than 80% DEGs in the necrotrophic stage. Both strains induced the least DEGs in the biotrophic stage compared to the initial invasion and necrotrophic stages. The orthologs of the effector genes Ecp6, PemG1, XEG1, ACE1, and Mg3LysM were exclusively induced by one of the two formae speciales depending on the infection stages. Some unigenes homologous to carbohydrate lytic enzyme genes, especially pectate lyases, were notably induced with multigermtubi forma specialis infection but not expressed in the monogermtubi forma specialis at an earlier infection stage. The extraordinary differences in the functional genome level between the two formae speciales of M. brunnea could be fundamental to exploring their host specificity determinant and evolution. This study also firstly provided the fungal transcriptome of the monogermtubi forma specialis for M. brunnea.

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“…Predicted proteins of C. tanaceti were used in downstream prediction of the secretome [90]. A combination of three software tools: SignalPv4.1 [91], Phobius [92] and WoLFPSORT [93] was used to predict the signal peptides.…”

Section: Prediction Of Secretome and Database Searches For Identifyinmentioning

confidence: 99%

Comparative genome analysis indicates rapid evolution of pathogenicity genes inColletotrichum tanaceti

Lelwala

Korhonen

Young

et al. 2019

Preprint

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23Colletotrichum tanaceti is an emerging foliar fungal pathogen of pyrethrum (Tanacetum 24 cinerariifolium), posing a threat to the global pyrethrum industry. Despite being reported 25 consistently from field surveys in Australia, the molecular basis of pathogenicity of C.26 tanaceti on pyrethrum is unknown. Herein, the genome of C. tanaceti (isolate BRIP57314) 27 was assembled de novo and annotated using transcriptomic evidence. The inferred 28 pathogenicity gene suite of C. tanaceti comprised a large array of genes encoding secreted 29 effectors, proteases, CAZymes and secondary metabolites. Comparative analysis of its 30 CAZyme pathogenicity profiles with those of closely related species suggested that C. 31tanaceti had additional hosts to pyrethrum. The genome of C. tanaceti had a high repeat 32 content and repetitive elements were located significantly closer to genes inferred to 33 influence pathogenicity than other genes. These repeats are likely to have accelerated 34 mutational and transposition rates in the genome, resulting in a rapid evolution of certain 35CAZyme families in this species. The C. tanaceti genome consisted of a gene-sparse, A-T 36 rich region facilitating a "two-speed" genome. Pathogenicity genes within this region were 37 likely to have a higher evolutionary rate than the 'core' genome. This "two-speed" genome 38 phenomenon in certain Colletotrichum spp. was hypothesized to have caused the clustering of 39 species based on the pathogenicity genes, to deviate from taxonomy. With the large repertoire 40 of pathogenicity factors that can potentially evolve rapidly in response to control measures, 41 C. tanaceti may pose a high-risk to global pyrethrum production. Knowledge of the 42 pathogenicity genes will facilitate future research in disease management of C. tanaceti and 43 other Colletotrichum spp.. 44 45 46 Evolution 65 tanaceti has been consistently reported in Australian field surveys of the crop [19] since 2013 66 [17] and causes leaf anthracnose, with black, water-soaked, sunken lesions [17]. Due to its 67 hemibiotrophic lifestyle, characteristic symptoms of C. tanaceti are not evident on leaves 68 until around 120 hours after infection [17, 20], when it switches from biotrophy to 69 necrotrophy. A significant reduction in green leaf area occurs usually 10 days after infection 70 [17]. This suggests a rapid disease cycle for C. tanaceti in pyrethrum and, given its 71 aggressiveness, the potential for serious crop damage. 4 72The molecular basis of pathogenicity of C. tanaceti, which includes the pathogenicity genes 73 and their evolution, has not been studied. Colletotrichum tanaceti has only been reported 74 from pyrethrum in Australia, but may have crossed over from another plant host species. 75However, cross-host pathogenicity has not yet been assessed and the pathogen's origin and 76 the potential host range are currently unknown. Therefore, the threat posed by C. tanaceti to 77 the local and global pyrethrum industry remains largely unknown. 78The genome sequence of an emer...

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FunSecKB2: a fungal protein subcellular location knowledgebase

Cited by 30 publications

References 41 publications

Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum

Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum

Distinctive Gene Expression Profiles and Effectors Consistent With Host Specificity in Two Formae Speciales of Marssonina brunnea

Comparative genome analysis indicates rapid evolution of pathogenicity genes inColletotrichum tanaceti

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