The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

/pdf/automated-eukaryotic-gene-structure-annotation-using-3fo28wpira.pdf

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

/pdf/notes-outline-and-divergence-times-of-basidiomycota-41rounhft0.pdf

Notes, outline and divergence times of Basidiomycota

The improved methods of heavy metals removal by biosorbents: A review.

Development of a flavor fingerprint by HS-GC-IMS with PCA for volatile compounds of Tricholoma matsutake Singer.

Macrofungus is defined as the fungus that grows an observable sporocarp. The sporocarps of many species are commonly called mushrooms and consumed by people all around the world as food and/or medicine. Most macrofungi belong to the divisions Basidiomycetes and Ascomycetes, which are estimated to contain more than 80,000 species in total. We report the draft genome assemblies of macrofungi (83 Basidiomycetes species and 7 Ascomycetes species) based on Illumina sequencing. The genome sizes of these species ranged from 27.4 Mb (Hygrophorus russula) to 202.2 MB (Chroogomphus rutilus). The numbers of protein-coding genes were predicted in the range of 9,511 (Hygrophorus russula) to 52,289 (Craterellus lutescens). This study provides the largest genomic dataset for macrofungi species. This resource will facilitate the artificial cultivation of edible mushrooms and the discovery of novel drug candidates.

/pdf/the-genome-sequences-of-90-mushrooms-2dcw05cwi2.pdf

The Genome Sequences of 90 Mushrooms.

Neuroprotective effect of crude polysaccharide isolated from the fruiting bodies of Morchella importuna against H2O2-induced PC12 cell cytotoxicity by reducing oxidative stress

Characterization and comparative mitogenomic analysis of six newly sequenced mitochondrial genomes from ectomycorrhizal fungi (Russula) and phylogenetic analysis of the Agaricomycetes.

In the present study, we assembled the mitogenomes of Pleurotus citrinopileatus and Pleurotus platypus. The circular mitogenome of the two Pleurotus species comprises a set of 14 conserved protein-encoding genes (PEGs), 2 RNA genes (small subunit ribosomal RNA and large subunit ribosomal RNA), and 24 tRNAs, with sizes of 60,694 and 73,807 bp, respectively. They contain 4 and 10 introns with 3 and 10 intronic open reading frames (ORFs), respectively. Thirteen position classes (Pcls) of introns were found in the cox1 gene of four Pleurotus species. The number and class of Pcl varied among different Pleurotus species, indicating that numerous events of loss and gain occurred during evolution of Pleurotus. Comparative mitogenomic and collinearity analyses reveal that large-scale gene rearrangements may have occurred during the evolution of Pleurotus citrinopileatus and Pleurotus platypus, including gene rearrangements and inversions, which may be related to the observed high amounts of repetitive DNA elements (5.62 and 5.45%, respectively). Phylogenetic analysis based on concatenated mitochondrial protein sequences reveals that concatenated mitochondrial genes are suitable as molecular markers for phylogenetic analysis. This serves as the first report on large-scale rearrangements in the mitochondria of the genus Pleurotus, thereby improving our understanding of the evolution of the Pleurotus genus and other macrofungi.

Comparative mitogenomics reveals large-scale gene rearrangements in the mitochondrial genome of two Pleurotus species

1-Octen-3-ol, known as mushroom alcohol, is a natural product extracted from fungi and plants. Its antimicrobial activities against five common food-related bacteria and two pathogenic fungi were evaluated in this paper, including Staphylococcus aureus, Bacillus subtilis, Staphylococcus epidermidis, Escherichia coli, Pseudomonas aeruginosa, Fusarium tricinctum and Fusarium oxysporum. The results showed that 1-octen-3-ol had a strong antibacterial activity against the tested bacteria, especially against Gram-positive bacteria, and it can also inhibit fungal growth and spore germination. The minimum inhibitory concentrations (MICs) for Gram-positive bacteria and Gram-negative bacteria were 1.0 and 2.0 mg/mL, respectively. The minimum bactericidal concentrations (MBCs) for Gram-positive bacteria and Gram-negative bacteria were 4.0 and 8.0 mg/mL, respectively. The completely inhibitory concentrations for fungal growth and spore germination were 8.0 and 2.0 mg/ml, respectively. Cell constituents' leakage and scanning electron microscope assays indicated that 1-octen-3-ol changed the permeability of the cell membrane. Discrepant antimicrobial activity between 1-octen-3-ol and 1-octen-3-one indicated that hydroxyl may play a decisive role in antimicrobial activity. It is suggested that 1-octen-3-ol, with attractive mushroom aroma and antimicrobial activity, has potential applications in control of pathogens.

https://www.jstage.jst.go.jp/article/jos/66/9/66_ess16196/_pdf

Wenli Huang

Papers

The Genome Sequences of 90 Mushrooms.

Neuroprotective effect of crude polysaccharide isolated from the fruiting bodies of Morchella importuna against H2O2-induced PC12 cell cytotoxicity by reducing oxidative stress

Characterization and comparative mitogenomic analysis of six newly sequenced mitochondrial genomes from ectomycorrhizal fungi (Russula) and phylogenetic analysis of the Agaricomycetes.

Comparative mitogenomics reveals large-scale gene rearrangements in the mitochondrial genome of two Pleurotus species

In vitro Antimicrobial Activities and Mechanism of 1-Octen-3-ol against Food-related Bacteria and Pathogenic Fungi.