Abstract
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.
Highlights
The fungal genus Mixia (Protomycetaceae, Taphrinales, Ascomycetes) was introduced by Kramer [1] based on a single species, Taphrina osmundae [2], parasitic on fronds of the Japanese royal fern Osmunda japonica in Japan
As we observed a loss of the longer peak at 150 nt in the highly transcribed (50 genes of highest level of expression) gene promoters of A. fumigatus [36], we examined whether the size of the mononucleosomes changes between the 50 genes of highest and lowest levels of expression in the upstream and downstream regions of the transcription start sites (TSSs)
By effectively using the high-throughput datasets of monoand dinucleosomal DNA fragments, we have identified characteristics of nucleosomal arrangement and linker DNA regions in the genome of the basidiomycete M. osmundae, which holds a unique phylogenic position in the evolution of fungal species
Summary
The fungal genus Mixia (Protomycetaceae, Taphrinales, Ascomycetes) was introduced by Kramer [1] based on a single species, Taphrina osmundae [2], parasitic on fronds of the Japanese royal fern Osmunda japonica in Japan. The new family Mixiaceae (Protomycetales) was proposed by Kramer [3] to accommodate the single genus Mixia In those days, almost all mycologists believed that Mixia is a member of the ascomycetes, related to the species of the Protomycetales or Taphrinales. According to the classification of Assembling the Fungal Tree of Life (AFTOL), at present, M. osmundae has been accommodated in the Mixiales, Mixiomycetes, Pucciniomycotina and Basidiomycota, [5] and has no close relatives [6]. 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]
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