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)

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

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Diet rapidly and reproducibly alters the human gut microbiome

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

/pdf/nuclear-ribosomal-internal-transcribed-spacer-its-region-as-9rhgb6gvih.pdf

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Several species in the Euwallacea fornicatus complex have emerged as important pests of woody plants globally, particularly in habitats where they are invasive aliens These beetles live in obligate symbioses with fungi in the genus Fusarium In this study, we identified Euwallacea spp and their fungal mutualists that have emerged as pests of planted Acacia crassicarpa in Riau, Indonesia Morphological identification and phylogenetic analyses of the mitochondrial cytochrome oxidase c subunit I (COI) gene confirmed that E similis and E perbrevis are the most abundant beetles infesting these trees Multilocus phylogenetic analyses of their fungal mutualists revealed their nonspecific association with six Fusarium species These included F rekanum and five novel Fusarium mutualists within the Fusarium solani species complex (FSSC), four of which reside in the Ambrosia Fusarium Clade (AFC) These new species are described here as F akasia, F awan, F mekan, F variasi, and F warna

Novel Fusarium mutualists of two Euwallacea species infesting Acacia crassicarpa in Indonesia.

Phytophthora pinifolia causes the needle and shoot disease of Pinus radiata in Chile known as Dano Foliar del Pino. Although P. pinifolia is primarily a needle pathogen, there are concerns that it might be spread to new environments via the export of contaminated timber. In order to determine whether P. pinifolia can enter or persist in green sawn lumber, its presence in lumber produced from trees exposed to the pathogen for at least four years was examined. Green lumber produced from the infected trees, and green wood samples artificially exposed to P. pinifolia inoculum, were analysed by making extensive isolations on Phytophthora selective media. In addition, PCR was conducted using species-specific primers developed for P. pinifolia. Results of the study showed that the green sawn lumber taken from trees infected by P. pinifolia, or green lumber exposed in infected pine plantations, displayed no evidence of the pathogen surviving in this material.

/pdf/potential-of-phytophthora-pinifolia-to-spread-via-sawn-green-3b14wyl5k7.pdf

Potential of Phytophthora pinifolia to spread via sawn green lumber: a preliminary investigation

The anamorph of Thyronectria austro-americana, a causal agent of honey locust canker, is shown to be Gyrostroma austro-americanum and Kaskaskia gleditsiae is reduced to synonymy.

Taxonomy of three canker-causing fungi of honey locust in the United States

The ophiostomatoid fungi are an economically important group that include various destructive plant pathogens. Knowledge regarding the occurrence of these fungi on larch (Larix spp.) and th...

Michael J. Wingfield

Papers

Novel Fusarium mutualists of two Euwallacea species infesting Acacia crassicarpa in Indonesia.

Potential of Phytophthora pinifolia to spread via sawn green lumber: a preliminary investigation

Taxonomy of three canker-causing fungi of honey locust in the United States

A new Ophiostoma species with a Graphium anamorph from Larix laricina in eastern North America

Phylogeny of theOphiostoma stenoceras–Sporothrix schenckiicomplex