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)

DNA sequencing with chain terminating inhibitors

Different types of molecules are discussed in relation to their fitness for providing the basis for a molecular phylogeny Best fit are the “semantides”, ie the different types of macromolecules that carry the genetic information or a very extensive translation thereof The fact that more than one coding triplet may code for a given amino acid residue in a polypeptide leads to the notion of “isosemantic substitutions” in genic and messenger polynucleotides Such substitutions lead to differences in nucleotide sequence that are not expressed by differences in amino acid sequence Some possible consequences of isosemanticism are discussed

Molecules as Documents of Evolutionary History

Some Sort of Species Certain populations of bacteria are known to show ecological differentiation, but how this happens has remained controversial. Shapiro et al. (p. 48; see the Perspective by Papke and Gogarten) examined whole-genome sequences from ecologically divergent Vibrio populations and found that genes and genome regions containing so-called “eco-SNPs” (single-nuleotide polymorphisms) have swept through populations. These regions differentiate the bacteria genetically, apparently according to the type of substratum on which they live. Subsequently, tight genotypic clusters may have emerged as a result of preferential recombination occurring within particular habitats. Although specialization into different habitats may reduce gene flow between bacterial populations, the bacteria will always remain open to taking up DNA from other populations and so they cannot be said to be species in the eukaryotic sense. Ecologically separated Vibrio populations diverge by gene-specific rather than genome-wide selective sweeps. Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

Wrinkles in the rare biosphere Kunin et al Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates Victor Kunin 1 , Anna Engelbrektson 1 , Howard Ochman 2 , and Philip Hugenholtz 1 Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA, 2 Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA Corresponding author: fax 925-296-5720 • email: phugenholtz@lblgov Email addresses: Victor Kunin: vkunin@lblgov Anna Engelbrektson: AEngelbrektson@lblgov Howard Ochman: hochman@emailarizonaedu Philip Hugenholtz: PHugenholtz@lblgov

Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates

Les picocyanobacteries du genre Synechococcus sont presentes dans tous les types d'environnements marins. Cette ubiquite s'explique en partie par la grande diversite pigmentaire de ces cellules, leur permettant de capturer efficacement la lumiere sur une large gamme spectrale. La plupart des souches ont une composition pigmentaire fixe mais certaines sont capables d'ajuster leur pigmentation en fonction de la lumiere incidente par un processus physiologique appele acclimatation chromatique de type IV (AC4). Une approche de metagenomique ciblee originale, combinant des techniques sophistiquees, a ete developpee afin d'etudier la diversite et la distribution des differents types pigmentaires de Synechococcus in situ. L'interet de cette approche a pu etre demontre apres des optimisations specifiques. La disponibilite de 25 nouveaux genomes de Synechococcus a permis de faire d'importantes avancees sur la comprehension du mecanisme d'AC4. Un cluster de 4 a 6 genes, codant pour une phycobiline-lyase et plusieurs regulateurs transcriptionnels, est systematiquement present chez toutes les souches capables de cette plasticite phenotypique. Deux configurations bien distinctes de ce cluster, nommees AC4-A et AC4-B, ont ete decouvertes et se retrouvent dans des lignees differentes de Synechococcus. Ces deux types de clusters auraient ete soumis a des processus evolutifs distincts. Par ailleurs, certaines singularites phenotypiques entre les souches possedant ces deux types de clusters genomiques ont pu etre demontrees. Ce travail de these souleve de nouvelles hypotheses sur la regulation de cette plasticite phenotypique ainsi que sur les mecanismes biochimiques associes.

Étude génomique, métagénomique et physiologique de la diversité pigmentaire chez les cyanobactéries du genre synechococcus

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Étude génomique, métagénomique et physiologique de la diversité pigmentaire chez les cyanobactéries du genre synechococcus