Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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

Cause, conseguenze e strategie di mitigazione Proponiamo il primo di una serie di articoli in cui affronteremo l’attuale problema dei mutamenti climatici. Presentiamo il documento redatto, votato e pubblicato dall’Ipcc - Comitato intergovernativo sui cambiamenti climatici - che illustra la sintesi delle ricerche svolte su questo tema rilevante.

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Climate Change 2007: The Physical Science Basis.

The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resume of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.

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The Top 10 fungal pathogens in molecular plant pathology

Many orchids have an obligate relationship with Tulasnella mycorrhizal fungi for seed germination and support into adulthood. Despite the importance of Tulasnella as mycorrhizal partners, many species remain undescribed. Here, we use multiple sequence locus phylogenetic analyses to delimit and describe six new Tulasnella species associated with Australian terrestrial orchids from the subtribes Cryptostylidinae and Drakaeinae. Five of the new species, Tulasnella australiensis, T. occidentalis, T. punctata, T. densa, and T. concentrica, all associate with Cryptostylis (Cryptostylidinae), whereas T. rosea associates with Spiculaea ciliata (Drakaeinae). Isolates representing T. australiensis were previously also reported in association with Arthrochilus (Drakaeinae). All newly described Tulasnella species were delimited by phylogenetic analyses of four loci (nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 [ITS], C14436 [ATP synthase], C4102 [glutamate synthase], and mt 16S rDNA [mtLSU]). The pairwise sequence divergence between species for the ITS region ranged from 5.6% to 25.2%, and the maximum sequence divergence within the newly described species ranged from 1.64% to 4.97%. There was a gap in the distribution of within- and between-species pairwise divergences in the region of 4-6%, with only one within-species value of 4.97% (for two T. australiensis isolates) and one between-species value of 5.6% (involving an isolate of T. occidentalis) falling within this region. Based on fluorescence staining, all six new Tulasnella species are binucleate and have septate, cylindrical hyphae. There was some subtle variation in culture morphology, but colony diameter as measured on 3MN+vitamin medium after 6 wk of growth did not differ among species. However, T. australiensis grew significantly (P < 0.02) slower than others on ½ FIM and ¼ potato dextrose agar (PDA) media. Formal description of these Tulasnella species contributes significantly to documentation of Tulasnella diversity and provides names and delimitations to underpin further research on the fungi and their relationships with orchids.

New species of Tulasnella associated with Australian terrestrial orchids in the Cryptostylidinae and Drakaeinae

Field surveys in 2006 confirmed that the exotic rust fungus Phragmidium violaceum was widespread on Rubus armeniacus and Rubus laciniatus in the Pacific Northwest of the USA. The origin and dispersal pattern of this obligate biotrophic pathogen in the USA were investigated by comparing the genetic diversity and structure of 27 isolates each from the USA and Europe, and 20 isolates from Australia where an invasion occurred in 1984. Analysis of 11 microsatellite loci revealed 74 unique genotypes, with the European population having a significantly higher level of allelic diversity and number of private alleles compared to populations from the USA and Australia. Principal coordinate analysis (PCA), analysis of molecular variance and pairwise comparisons of Φ confirmed a strong level of differentiation among continental populations, with little divergence between isolates from the USA and Europe, but a high level of differentiation between these isolates and those from Australia. These results were broadly supported by the Bayesian cluster analysis, which indicated that at K = 3 the clustering of the isolates corresponds to their geographic origin. Bayesian clustering, PCA as well as insignificant migration estimates from Europe to the USA suggest that the USA population is not a direct descendant from the European P. violaceum population. There was a weak association between genetic and geographic distance among the USA isolates, suggesting invasion was initially localized prior to dispersal or that the population may have been present for some time prior to first detection in 2005.

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Invaded range of the blackberry pathogen Phragmidium violaceum in the Pacific Northwest of the USA and the search for its provenance

Pathogens evolve in an arms race, frequently evolving virulence that defeats resistance genes in their hosts. Infection of multiple hosts may accelerate this virulence evolution. Theory predicts that host diversity affects pathogen diversity, with more diverse hosts expected to harbour more diverse pathogens that reproduce sexually. We tested this hypothesis by comparing the microsatellite (SSR) genetic diversity of the barley leaf pathogen Pyrenophora teres f. teres (Ptt) from barley (monoculture) and barley grass (outbreeding). We also aim to investigate host specificity and attempt to track virulence on two barley cultivars, Maritime and Keel. Genetic diversity in barley Ptt populations was higher than in populations from barley grass. Barley Ptt populations also had higher linkage disequilibrium levels, indicating less frequent sexual reproduction, consistent with the Red Queen hypothesis theory that genetically diverse hosts should select for higher levels of sexual reproduction of the pathogen. SSR analyses indicate that host-associated Ptt populations do not share genotypes and have independent evolutionary histories. Pathogenicity studies showed host specificity as host-associated Ptt isolates could not cross-infect hosts. Minimum spanning network analyses indicated two major clusters of barley Ptt. One cluster represents Maritime virulent and isolates from Western Australia (WA). Low PhiPt population differentiation between WA populations and those from Maritime and Keel, indicated a WA origin of the Maritime and Keel virulences. The main minimum spanning network cluster is represented by a panmictic population structure, represented by isolates from all over Australia. Although barley Ptt populations are more diverse than barley grass Ptt populations, this may be a result of the size and number of founder Ptt populations to Australia, with larger and more barley Ptt populations introduced. More frequent sexual reproduction of Ptt on barley grass support the Red Queen Hypothesis and suggest evolutionary potential of pathogens on diverse hosts are high. Extensive gene flow of Ptt between regions in Australia is suggested to maintain a panmictic population structure, with human-mediated dispersal aiding in virulence evolution of Ptt on barley.

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Host specialisation and disparate evolution of Pyrenophora teres f. teres on barley and barley grass.

Pathogen evolution in response to host resistance genes: Evidence from fields experiments with Rhynchosporium secalis on barley

The population structure and genotypic diversity of Septoria tritici Rob ex Desm. from two crop field populations in Buenos Aires Province were studied with DNA restriction fragment length polymorphism. Hierarchical samples were taken from different cultivars. A total of 120 single spore isolates was subject to molecular analysis to compare the genetic structure of Los Hornos and Balcarce populations separated by 500km. Eight RFLP loci and 1DNA fingerprinting were used. Among the total of the isolates, 24 RFLP alleles were detected from the first population and 22 from the second. Gene and genotype diversity were high in both populations. Different haplotypes for each region were identified. Identical haplotypes were clustered in the same location in the field. The mean gene diversity and the mean genotypic diversity were high for the 8 loci of RFLP. This means that Balcarce and Los Hornos were significantly different. The X2 was significant (P>0.005) only for two RFLP locus, then both populations were not independant. They had to be compared with an European and an American populations. Balcarce population was very different to all of them. Both Argentine populations were very similar at regional level but strongly different at a continental level. The greatest genetic variability between continents belonged to Argentine population. The amount of gene flow was high when all the populations were compared.

Celeste C. Linde

Papers

New species of Tulasnella associated with Australian terrestrial orchids in the Cryptostylidinae and Drakaeinae

Invaded range of the blackberry pathogen Phragmidium violaceum in the Pacific Northwest of the USA and the search for its provenance

Host specialisation and disparate evolution of Pyrenophora teres f. teres on barley and barley grass.

Pathogen evolution in response to host resistance genes: Evidence from fields experiments with Rhynchosporium secalis on barley

Genotypic Diversity of the Wheat leaf blotch pathogen ( Septoria tritici ) in Buenos Aires Province