Draft genome sequencing of the enigmatic basidiomycete Mixia osmundae

Nishida, Hiromi; Nagatsuka, Yuka; Sugiyama, Junta

doi:10.2323/jgam.57.63

Cited by 8 publications

(3 citation statements)

References 16 publications

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“…It takes a unique position in basidiomycete phylogeny as an enigmatic fungus. We previously reported an initial genome assembly of this species comprising 4408 contigs (a total of 3 019 501 nt) [7]. …”

Section: Introductionmentioning

confidence: 99%

Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping

Nishida

Kondo²,

Matsumoto

et al. 2012

Open Biol.

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We present findings on the nucleosomal arrangement in the genome of the basidiomycete Mixia osmundae, focusing on nucleosomal linker DNA regions. We have assembled the genomic sequences of M. osmundae, annotated genes and transcription start sites (TSSs) on the genome, and created a detailed nucleosome map based on sequencing mono- and dinucleosomal DNA fragments. The nucleosomal DNA length distribution of M. osmundae is similar to that of the filamentous ascomycete Aspergillus fumigatus, but differs from that of ascomycetous yeasts, strongly suggesting that nucleosome positioning has evolved primarily through neutral drift in fungal species. We found clear association between dinucleotide frequencies and linker DNA regions mapped as the midpoints of dinucleosomes. We also describe a unique pattern found in the nucleosome-depleted region upstream of the TSS observed in the dinucleosome map and the precursor status of dinucleosomes prior to the digestion into mononucleosomes by comparing the mono- and dinucleosome maps. We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome.

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Section: Introductionmentioning

confidence: 99%

Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping

Nishida

Kondo²,

Matsumoto

et al. 2012

Open Biol.

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“…Besides, the ferroxidase-type protein E5Q_00257 from Mixia osmundae IAM 14324 was recurrently found in both dye-decolorizing and laccase-induced EPPs. This enigmatic fungus, the only species currently known in class Mixiomycetes, is an intracellular parasite of ferns ( Osmunda L ) in which it causes small yellow to brown leaf spots [ 46 ]. Iron acquisition is a critical aspect of the virulence of many pathogenic microbes.…”

Section: Discussionmentioning

confidence: 99%

Identification and characterization of laccase-type multicopper oxidases involved in dye-decolorization by the fungus Leptosphaerulina sp.

et al. 2015

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BackgroundFungal laccases are multicopper oxidases (MCOs) with high biotechnological potential due to their capability to oxidize a wide range of aromatic contaminants using oxygen from the air. Albeit the numerous laccase-like genes described in ascomycete fungi, ascomycete laccases have been less thoroughly studied than white-rot basidiomycetous laccases. A variety of MCO genes has recently been discovered in plant pathogenic ascomycete fungi, however little is known about the presence and function of laccases in these fungi or their potential use as biocatalysts. We aim here to identify the laccase-type oxidoreductases that might be involved in the decolorization of dyes by Leptosphaerulina sp. and to characterize them as potential biotechnological tools.ResultsA Leptosphaerulina fungal strain, isolated from lignocellulosic material in Colombia, produces laccase as the main ligninolytic oxidoreductase activity during decolorization of synthetic organic dyes. Four laccase-type MCO genes were partially amplified from the genomic DNA using degenerate primers based on laccase-specific signature sequences. The phylogenetic analysis showed the clustering of Lac1, Lac4 and Lac3 with ascomycete laccases, whereas Lac2 grouped with fungal ferroxidases (together with other hypothetical laccases). Lac3, the main laccase produced by Leptosphaerulina sp. in dye decolorizing and laccase-induced cultures (according to the shotgun analysis of both secretomes) was purified and characterized in this study. It is a sensu-stricto laccase able to decolorize synthetic organic dyes with high efficiency particularly in the presence of natural mediator compounds.ConclusionsThe searching for laccase-type MCOs in ascomycetous families where their presence is poorly known, might provide a source of biocatalysts with potential biotechnological interest and shed light on their role in the fungus. The information provided by the use of genomic and proteomic tools must be combined with the biochemical evaluation of the enzyme to prove its catalytic activity and applicability potential.Electronic supplementary materialThe online version of this article (doi:10.1186/s12896-015-0192-2) contains supplementary material, which is available to authorized users.

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“…(Microbotryales)) (Cantu et al ., ; Duplessis et al ., ; Kumar et al ., ; http://www.jgi.doe.gov/fungi; http://www.broadinstitute.com; http://www.ncbi.nlm.nih.gov). Thus, of the nine classes and 20 orders described to date within Pucciniomycotina (Schell et al ., ; Toome et al ., ; Aime et al ., ), complete annotated genomes are only available for two classes and three orders; some incomplete and unannotated genomic data are available for seven additional Pucciniomycotina species – six additional rust fungi and a draft genome for M. osmundae (Nishida et al ., ; http://www.ncbi.nlm.nih.gov).…”

Section: Introductionmentioning

confidence: 99%

Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogenMixia 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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Draft genome sequencing of the enigmatic basidiomycete Mixia osmundae

Cited by 8 publications

References 16 publications

Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping

Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping

Identification and characterization of laccase-type multicopper oxidases involved in dye-decolorization by the fungus Leptosphaerulina sp.

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

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