A New Omics Data Resource of Pleurocybella porrigens for Gene Discovery

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 FindingsShort 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.ConclusionsFunctional 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.

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants

“…Publically available non-Salix RNA-seq data used for forced mapping were acquired from Homo sapiens (human, EBI: PRJEB6971); Pleurocybella porrigens (angel wing fungi, EBI: DRR003995; EBI: DRR003996; Suzuki et al, 2013); Carassius auratus (goldfish, EBI: DRR014529; Abe et al, 2014); Oryza sativa (rice, EBI: SRR611648); and Mammuthus primigenius (woolly mammoth; DNA-seq, EBI: SRR2009641; EBI SRR2009644; Lynch et al, 2015).…”

A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel’s wing oyster mushroom, Sugihiratake)

“…To disclose the genes underlying the poisonings and provide mechanistic insight, we have sought to develop an information infrastructure containing omics data. In a previous study, we sequenced the genome and transcriptome of the mushroom using next-generation sequencing techniques [ 12 ]. That study revealed that, compared to other Agaricales, the genome of the angel’s wing had a unique structure and contained numerous novel genes.…”

Reaping the Benefits of Next-generation Sequencing Technologies for Crop Improvement — Solanaceae

“…The recent advances in crop genomics, particularly the use of high throughput next-generation sequencing (NGS) technologies, look promising to identify causal genetic factors at genome by sequencing the whole genome and transcriptome of a species. As a result, the complete gene catalogue of a crop species and functional genes in different tissues could be identified besides allowing studying the genetic pathways involved in growth and development and biochemical pathways that eventually could be correlated with the crop phenotypes [1,2]. Furthermore, the sequence data generated in vast amount provide a basis of genetic variation such as singlenucleotide polymorphisms (SNPs), which ultimately provide a relationship between genotype and phenotype in different species.…”