Fungal Genomic Annotation

Grigoriev, Igor V.; Martínez, Diego; Salamov, Asaf

doi:10.1016/s1874-5334(06)80008-0

Cited by 31 publications

(31 citation statements)

References 72 publications

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“…P. ostreatus was sequenced with the Sanger whole-genome shotgun approach and assembled with Arachne (76). All genomes were annotated using the JGI Annotation Pipeline (77), which combines several gene prediction and annotation methods with transcriptomics data, and integrates the annotated genomes into MycoCosm (78), a Web-based fungal resource for comparative analysis. Protein Sequence Clustering.…”

Section: Methodsmentioning

confidence: 99%

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Riley

Salamov

Brown

et al. 2014

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

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598

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Significance Wood decay fungi have historically been characterized as either white rot, which degrade all components of plant cell walls, including lignin, or brown rot, which leave lignin largely intact. Genomic analyses have shown that white-rot species possess multiple lignin-degrading peroxidases (PODs) and expanded suites of enzymes attacking crystalline cellulose. To test the adequacy of the white/brown-rot categories, we analyzed 33 fungal genomes. Some species lack PODs, and thus resemble brown-rot fungi, but possess the cellulose-degrading apparatus typical of white-rot fungi. Moreover, they appear to degrade lignin, based on decay analyses on wood wafers. Our results indicate that the prevailing paradigm of white rot vs. brown rot does not capture the diversity of fungal wood decay mechanisms.

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Section: Methodsmentioning

confidence: 99%

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Riley

Salamov

Brown

et al. 2014

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

Self Cite

598

540

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“…Both genomes were annotated using the JGI annotation pipeline (Grigoriev et al, 2006), which combines several gene prediction and functional annotation methods with transcriptome data and integrates the result in Mycocosm (Grigoriev et al, 2014), a web-based resource for fungal comparative genomics. Before gene prediction, assembly scaffolds were masked using RepeatMasker (http://www.repeatmasker.org), RepBase library (Jurka et al, 2005), and frequent (>150 times) repeats were recognized by RepeatScout (Price et el., 2005).…”

Section: Methodsmentioning

confidence: 99%

Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii

Floudas

Held

Riley

et al. 2015

Fungal Genetics and Biology

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142

130

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Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white rot fungus Cylindrobasidium torrendii and the brown rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. Cylindrobasidium torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C. torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. Fistulina hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition towards a brown rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited.

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“…The genome was annotated using the JGI annotation Pipeline (Grigoriev et al ., ), which combines several gene prediction and annotation methods, and integrates the annotated genome into the web‐based fungal resource MycoCosm (Grigoriev et al ., ) for comparative genomics. Genome assembly and annotations can be interactively accessed through the JGI fungal genome portal MycoCosm (Grigoriev et al ., ) at http://jgi.doe.gov/Mosmundae and have also been deposited to DDBJ/EMBL/GenBank under accession no.…”

Section: Methodsmentioning

confidence: 99%

Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae

et al. 2013

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SummaryMixia osmundae (Basidiomycota, Pucciniomycotina) represents a monotypic class containing an unusual fern pathogen with incompletely understood biology. We sequenced and analyzed the genome of M. osmundae, focusing on genes that may provide some insight into its mode of pathogenicity and reproductive biology.Mixia osmundae has the smallest plant pathogenic basidiomycete genome sequenced to date, at 13.6 Mb, with very few repeats, high gene density, and relatively few significant gene family gains.The genome shows that the yeast state of M. osmundae is haploid and the lack of segregation of mating genes suggests that the spores produced on Osmunda spp. fronds are probably asexual. However, our finding of a complete complement of mating and meiosis genes suggests the capacity to undergo sexual reproduction. Analyses of carbohydrate active enzymes suggest that this fungus is a biotroph with the ability to break down several plant cell wall components.Analyses of publicly available sequence data show that other Mixia members may exist on other plant hosts and with a broader distribution than previously known.

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Fungal Genomic Annotation

Cited by 31 publications

References 72 publications

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii

Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae

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