FUNYBASE: a FUNgal phYlogenomic dataBASE

Marthey, Sylvain; Aguileta, Gabriela; Rodolphe, F.; Gendrault, Annie; Giraud, Tatiana; Fournier, Elisabeth; López‐Villavicencio, Manuela; Gautier, Angélique; Lebrun, Marc; Chiapello, Hélène

doi:10.1186/1471-2105-9-456

Cited by 63 publications

(61 citation statements)

References 27 publications

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“…The predicted protein sets were searched for highly conserved single-(low) copy genes to assess the completeness of the genomic sequences and gene predictions. Orthologous genes to all 246 single-copy genes were searched for all proteomes by blastp comparisons (eVal: 10-3) against the single-copy families from all 21 species available from the FunyBASE 56 . Additionally, the proteomes were searched for the 248 core genes commonly present in higher eukaryotes (CEGs) by Blastp comparisons (eVal: 10-3) 57 .…”

Section: Methodsmentioning

confidence: 99%

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

et al. 2017

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T he genus Armillaria causes root rot disease in both gymnoand angiosperms, in forests, parks, and even vineyards in more than 500 host plant species 1 across the world. Most Armillaria species are facultative necrotrophs, which, after colonizing and killing the root cambium, transition to a saprobic phase, decomposing dead woody tissues of the host. As saprotrophs, Armillaria spp. are white rot (WR) fungi, which can efficiently decompose all components of plant cell walls, including lignin, (hemi-)cellulose and pectin 2 . They produce fleshy fruiting bodies (honey mushrooms) that appear in large clumps around infected plants and produce sexual spores. The vegetative phase of Armillaria is predominantly diploid rather than dikaryotic like most basidiomycetes.Individuals of Armillaria can reach immense sizes and include the 'humongous fungus' , one of the largest terrestrial organisms on Earth 3 , measuring up to 965 hectares and 600 tons 4 , and can display a mutation rate ≅ 3 orders of magnitude lower than most filamentous fungi 5 . Individuals reach this immense size via growing rhizomorphs, dark mycelial strings 1-4 mm wide that allow the fungus to bridge gaps between food sources or host plants 1,6 (hence the name shoestring root rot). Rhizomorphs develop through the aggregation and coordinated parallel growth of hyphae, similar to some fruiting body tissues 7,8 . As migratory and exploratory organs, rhizomorphs can grow approximately 1 m yr −1 and cross several metres underground in search for new hosts, although roles in uptake and longrange translocation of nutrients have also been proposed 1,9,10 . Root contact by rhizomorphs is the main mode of infection by the fungus, which makes the prevention of recurrent infection in Armillariacontaminated areas particularly difficult 1 . Despite their huge impact on forestry, horticulture and agriculture, the genetics of the pathogenicity of Armillaria species is poorly understood. The only -omics data published so far have highlighted a substantial repertoire of plant cell wall degrading enzymes (PCWDE) and secreted proteins, among others, in A. mellea and A. solidipes 11,12 , while analyses of the genomes of other pathogenic basidiomycetes (such as Moniliophthora 13,14 , Heterobasidion 15 and Rhizoctonia 16 ) identified genes coding for PCWDEs, secreted and effector proteins or secondary metabolism (SM) as putative pathogenicity factors. However, the lifecycle and unique dispersal strategy of Armillaria prefigure other evolutionary routes to pathogenicity, which, along with other potential genomic factors (such as transposable elements 17 ) are not yet known.Here, we investigate genome evolution and the origin of pathogenicity in Armillaria using comparative genomics, transcriptomics

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Section: Methodsmentioning

confidence: 99%

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

et al. 2017

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“…All of the 248 CEGs were present in our curated gene set with full HMM domain coverage. On the other hand, FUNYBASE (FUNgal phYlogenomic dataBASE) 17 provides 246 single-copy ortholog clusters in 21 sequenced fungal genomes. We extracted these single-copy protein sequences from the FUNYBASE website and built the HMM model for each cluster.…”

Section: Methodsmentioning

confidence: 99%

“…The protein-coding genes occupy 80% of the genome sequence. According to recently proposed measures for genome completeness, we searched the genome for highly conserved single (or low) copy gene sets: core eukaryotic genes (CEGs) with 248 genes across six model organisms 16 and FUNYBASE 17 with 246 genes with orthologs in 21 fungi. All genes from both gene sets were present in our proteome with full domain coverage.…”

Section: Pichia Pastoris Phylogenetic Positionmentioning

confidence: 99%

Genome sequence of the recombinant protein production host Pichia pastoris

et al. 2009

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The methylotrophic yeast Pichia pastoris is widely used for the production of proteins and as a model organism for studying peroxisomal biogenesis and methanol assimilation. P. pastoris strains capable of human-type N-glycosylation are now available, which increases the utility of this organism for biopharmaceutical production. Despite its biotechnological importance, relatively few genetic tools or engineered strains have been generated for P. pastoris. To facilitate progress in these areas, we present the 9.43 Mbp genomic sequence of the GS115 strain of P. pastoris. We also provide manually curated annotation for its 5,313 protein-coding genes.The methylotrophic yeast Pichia pastoris is by far the most commonly used yeast species in the production of recombinant proteins 1 and is employed in laboratories around the world to produce proteins for basic research and medical applications. It is also an important model organism for the investigation of peroxisomal proliferation and methanol assimilation. The P. pastoris expression technology has been commercially available for many years. P. pastoris grows to high cell density, provides tightly controlled methanol-inducible transgene expression and efficiently secretes heterologous proteins in defined media. Several P. pastoris-produced biopharmaceuticals that are either not glycosylated (such as human serum albumin 2 ) or for which glycosylation is needed only for proper folding (such as several vaccines 3 ) are already on the market. An important recent breakthrough has been the development of P. pastoris strains with humantype N-glycosylation [4][5][6] . Humanized glycosylation will further increase the importance of P. pastoris for biopharmaceutical production; indeed, proteins produced with this system are moving into clinical development 7 . Moreover, monoclonal antibodies can be made at gramper-liter scale in the humanized glycosylation-homogenous strains 8 .For further strain engineering, a better understanding of all aspects of the yeast's protein production machinery is needed, and a number of studies relating to P. pastoris's secretory system and engineered promoters have been forthcoming 9,10 . To facilitate the investigation of P. pastoris and other methylotrophic yeasts, we present the 9.43 Mbp genomic sequence of the GS115 strain of P. pastoris.

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“…Sequencing of the highly polymorphic MRR1 gene revealed that group S isolates show more than 4 % divergence from B. cinerea strains B05.10 and T4, which have MRR1 genes with 99.9 % identity. Further sequencing of HSP60 and NEP2, and of two FUNYBASE genes that are suitable for phylogenetic studies (Marthey et al 2008), partially supported the genetic separation of group S isolates (Johnston et al 2013;Leroch et al 2013). Genome sequencing of several B. cinerea and group S strains, and the analysis of additional polymorphic genes in isolates collected from various host plants in different countries, revealed at least two subclades that could be separated from the common B. cinerea genotype (Plesken and Hahn, unpublished).…”

Section: Species Identification and Numbersmentioning

confidence: 99%

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

et al. 2014

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Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineagespecific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae,

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FUNYBASE: a FUNgal phYlogenomic dataBASE

Cited by 63 publications

References 27 publications

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Genome sequence of the recombinant protein production host Pichia pastoris

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

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