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A New Omics Data Resource of Pleurocybella Porrigens for Gene Discovery

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A New Omics Data Resource of Pleurocybella Porrigens for Gene Discovery A New Omics Data Resource of Pleurocybella porrigens for Gene Discovery Tomohiro Suzuki1☯, Kaori Igarashi2☯, Hideo Dohra3, Takumi Someya2, Tomoyuki Takano2, Kiyonori Harada2, Saori Omae4, Hirofumi Hirai4, Kentaro Yano2*, Hirokazu Kawagishi1,4* 1 Graduate School of Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan, 2 Bioinformatics Laboratory, School of Agriculture, Meiji University, Kawasaki, Japan, 3 Institute for Genetic Research and Biotechnology, Shizuoka University, Suruga-ku, Shizuoka, Japan, 4 Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka, Japan Abstract Background: Pleurocybella porrigens is a mushroom-forming fungus, which has been consumed as a traditional food in Japan. In 2004, 55 people were poisoned by eating the mushroom and 17 people among them died of acute encephalopathy. Since then, the Japanese government has been alerting Japanese people to take precautions against eating the P. porrigens mushroom. Unfortunately, despite efforts, the molecular mechanism of the encephalopathy remains elusive. The genome and transcriptome sequence data of P. porrigens and the related species, however, are not stored in the public database. To gain the omics data in P. porrigens, we sequenced genome and transcriptome of its fruiting bodies and mycelia by next generation sequencing. Methodology/Principal Findings: Short read sequences of genomic DNAs and mRNAs in P. porrigens were generated by Illumina Genome Analyzer. Genome short reads were de novo assembled into scaffolds using Velvet. Comparisons of genome signatures among Agaricales showed that P. porrigens has a unique genome signature. Transcriptome sequences were assembled into contigs (unigenes). Biological functions of unigenes were predicted by Gene Ontology and KEGG pathway analyses. The majority of unigenes would be novel genes without significant counterparts in the public omics databases. Conclusions: Functional analyses of unigenes present the existence of numerous novel genes in the basidiomycetes division. The results mean that the omics information such as genome, transcriptome and metabolome in basidiomycetes is short in the current databases. The large-scale omics information on P. porrigens, provided from this research, will give a new data resource for gene discovery in basidiomycetes. Citation: Suzuki T, Igarashi K, Dohra H, Someya T, Takano T, et al. (2013) A New Omics Data Resource of Pleurocybella porrigens for Gene Discovery. PLoS ONE 8(7): e69681. doi:10.1371/journal.pone.0069681 Editor: Mikael Rørdam Andersen, Technical University of Denmark, Denmark Received October 11, 2012; Accepted June 14, 2013; Published July 23, 2013 Copyright: © 2013 Suzuki et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was partially supported by a Grant-in-Aid for Research and Development Projects for Application in Promoting New Policy of Agriculture Forestry and Fisheries from MAFF, a Grant-in-Aid for Scientific Research on Innovative Areas “Chemical Biology of Natural Products” from MEXT (Grant Number 24102513), and a Grant-in-Aid for Scientific Research (A) from JSPS (Grant Number 24248021) to H.K. This work was also supported in part by a Grant in-Aid for Scientific Research on Innovative Areas (No. 24113518) from MEXT, A-STEP (AS232Z02832E) and CREST from JST, Research Funding for Computational Software Supporting Program from Meiji University, and a Grant-in-Aid for Scientific Research (A) (23248005) and Scientific Research (B) (20380023) from JSPS to K.Y. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. * E-mail: [email protected]; (HK) [email protected] (KY) ☯ These authors contributed equally to this work. Introduction been identified so far [4]. Hawksworth et al. (2001) has inferred that around 140,000 species of mushrooms-forming fungi exist In eukarya, fungus is a huge group consisting of various on Earth [5]. Identification of the characteristics of various microorganisms such as yeasts, molds and mushrooms. To mushrooms species facilitates a more efficient and effective date, about 69,000 fungal species have been identified and utilization as nutrient and medicinal resources [6]. It also helps reported. However, the total number of fungal species in the to understand the structure and dynamics of complex world is estimated at around 1.5 million [1]. In mushroom- ecological systems. forming fungi, which have economic values as edible and A basidiomycete Pleurocybella porrigens (division : medicinal resources for human [2,3], 21,000 species have Basidiomycota, order : Agaricales) is a mushroom-forming PLOS ONE | www.plosone.org 1 July 2013 | Volume 8 | Issue 7 | e69681 An Omics Data Resource of Pleurocybella porrigens fungus, which has been consumed as a traditional food in Table 1. The numbers of sequencing reads. Japan. In 2004, however, 55 people were poisoned by eating the mushroom and 17 people among them died of acute encephalopathy. Since then, the Japanese government has Number of high-quality been alerting Japanese people to take precautions against Library Number of raw reads reads eating the P. porrigens mushroom. Ever since the food- Genome (PE reads) 60,919,280 50,292,262 poisoning incident, we have been trying to understand the Genome (MP reads) 83,048,614 59,947,894 molecular mechanism for the acute encephalopathy and have Transcriptome of fruiting 75,071,884 51,405,754 reported the isolation and characterization of a lectin and bodies (PE reads) unusual amino acids from the mushroom, which might be Transcriptome of mycelia 69,747,206 50,806,810 related to the accident [7–9]. There are also some papers (PE reads) concerning the mushroom reported by other researchers [10–12]. However, the real truth of the molecular mechanism for the acute encephalopathy still remains elusive. Table 2. Assembly summary. Conventionally, isolations of toxins produced from mushrooms have been studied using bioassays measuring their intrinsic toxicity. For example, Matsuura et al. (2009) have A. Genome isolated cycloprop-2-ene carboxylic acid from the lethal Number of scaffolds 31,164 mushroom Russula subnigricans [13]. This compound is lethal Total size of scaffolds (bp) 32,149,440 at 2.5 mg/kg by oral administration against mice. We have also N50 (bp) 1,598 reported the isolation and characterization of a family of Average scaffold length (bp) 1,032 isolectins (Boletus venenatus lectins, BVLs) from the Maximum scaffold length (bp) 22,324 diarrheagenic mushroom B. venenatus [14]. Oral administration Minimum scaffold length (bp) 173 of BVLs caused diarrhea in rats. However, all the compounds B. Transcriptome obtained from the mushroom P. porrigens did not cause acute Fruiting bodies Mycelia encephalopathy in animals. This might be due to unkown Number of contigs 45,390 26,216 mechanism involved in causing toxicity than that of usual Total size of contigs (bp) 29,504,308 11,748,163 toxicity mentioned above. The omics data such as genome and N50 (bp) 1,069 633 transcriptome data improve our abilities to analyze biological Average contig length (bp) 650 448 functions of toxicity from P. porrigens. Maximum contig length (bp) 9,955 8,825 Public database for omics data on fungi ‘The Fungal Minimum contig length (bp) 100 100 Genome Initiative’ (http://www.broad.mit.edu/annotation/fgi/) at the Broad Institute provides genome sequences information for site(s) from the raw Illumina sequencing data. Genome more than 50 fungal genomes [15]. However, the genome and sequence reads, 50,292,262 (82.6%) PE reads and 59,947,894 transcriptome sequence data of P. porrigens and the related (72.2%) MP reads which were pre-processed were employed species are not stored in the public database. To gain the for further analysis. 51,405,754 (68.5%) transcriptome omics data and knowledge in P. porrigens, sequenced genome sequence reads of the fruiting bodies and 50,806,810 (72.8%) and transcriptome data of fruiting bodies and mycelia by next transcriptome sequence reads of mycelia which were pre- generation sequencing is reported here. The computational processed were also employed for further analysis (Table 1). analysis was also performed to predict biological functions of each transcript. The large-scale omics data in P. porrigens De novo assembly open new avenues to advance our understanding of fungal We assembled the high-quality genomic DNA sequences species. into scaffolds. We used the program Velvet [16] to assemble reads, since Velvet investigates and eliminates the Results and Discussion contamination of MP reads (see the Velvet manual in detail). The assembling of PE reads by Velvet provided contigs; the Sequencing of genomic DNAs and mRNAs largest N50 contig length of 931 bp under k=81. With the Short read sequences (100 bp in length) of genomic DNAs contigs and MP reads (3 kb insert size library), we obtained and mRNAs in P. porrigens were generated by Illumina scaffolds by assembling (Table 2A). The largest N50 length Genome Analyzer (Table 1). The short read sequences from (1598 bp) was obtained under k=87. The range of the scaffold genomic DNAs contain 60,919,280 paired-end (PE) sequence lengths was 173 to 22,324 bp (the average length was 1,032 reads (30,459,640 pairs) and 83,048,614 mate-paired (MP) bp). reads (41,524,307 pairs). PE reads from mRNAs were also The high-quality short reads from mRNAs were assembled generated; 75,071,884 reads (37,535,942 pairs) in the fruiting into unigenes (contigs, a non-redundant sequence set) by the bodies and 69,747,206 reads (34,873,603 pairs) in the mycelia. program Oases [17]. To avoid confusion in the terminology, the We obtained high-quality read sequences by removing contigs obtained from transcriptome sequences are referred to regions with low quality scores in fastq files (quality scores < as ‘unigenes’.
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