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

We constructed nine sets of oligonucleotide primers on the basis of the results of DNA hybridization of cloned genes from Neurospora crassa and Aspergillus nidulans to the genomes of select filamentous ascomycetes and deuteromycetes (with filamentous ascomycete affiliations). Nine sets of primers were designed to amplify segments of DNA that span one or more introns in conserved genes. PCR DNA amplification with the nine primer sets with genomic DNA from ascomycetes, deuteromycetes, basidiomycetes, and plants revealed that five of the primer sets amplified a product only from DNA of the filamentous ascomycetes and deuteromycetes. The five primer sets were constructed from the N. crassa genes for histone 3, histone 4, beta-tubulin, and the plasma membrane ATPase. With these five primer sets, polymorphisms were observed in both the size of and restriction enzyme sites in the amplified products from the filamentous ascomycetes. The primer sets described here may provide useful tools for phylogenetic studies and genome analyses in filamentous ascomycetes and deuteromycetes (with ascomycete affiliations), as well as for the rapid differentiation of fungal species by PCR.

Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes.

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.

/pdf/the-top-10-fungal-pathogens-in-molecular-plant-pathology-4nidxj1xqt.pdf

The Top 10 fungal pathogens in molecular plant pathology

▪ Abstract We hypothesize that the evolutionary potential of a pathogen population is reflected in its population genetic structure. Pathogen populations with a high evolutionary potential are more likely to overcome genetic resistance than pathogen populations with a low evolutionary potential. We propose a flexible framework to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure. According to this framework, pathogens that pose the greatest risk of breaking down resistance genes have a mixed reproduction system, a high potential for genotype flow, large effective population sizes, and high mutation rates. The lowest risk pathogens are those with strict asexual reproduction, low potential for gene flow, small effective population sizes, and low mutation rates. We present examples of high-risk and low-risk pathogens. We propose general guidelines for a rational approach to breed durable resistance according to the evolutionary potential of the pathogen.

Pathogen population genetics, evolutionary potential, and durable resistance

New diseases of humans, animals and plants emerge regularly. Enhanced virulence on a new host can be facilitated by the acquisition of novel virulence factors. Interspecific gene transfer is known to be a source of such virulence factors in bacterial pathogens (often manifested as pathogenicity islands in the recipient organism) and it has been speculated that interspecific transfer of virulence factors may occur in fungal pathogens. Until now, no direct support has been available for this hypothesis. Here we present evidence that a gene encoding a critical virulence factor was transferred from one species of fungal pathogen to another. This gene transfer probably occurred just before 1941, creating a pathogen population with significantly enhanced virulence and leading to the emergence of a new damaging disease of wheat.

Emergence of a new disease as a result of interspecific virulence gene transfer.

The idea that theory developed in the fields of population genetics and evolutionary biology can be used to investigate and understand problems in plant pathology has not been widely accepted. Today, although one can cite exceptions (3, 26, 57, 78), only a small fraction of the efforts in plant pathology are devoted to investigating the population genetics of plant pathogens. Even more recent is the use of DNA markers to examine the population dynamics of plant pathogens. This development is providing levels of precision not previously available and may revolutionize the analysis of the population biology of plant pathogens. Though population genetics encom­ passes a diverse array of evolutionary processes and their interactions, in this review we consider only the role of the temporal and spatial movement of genes and genotypes on the population dynamics and evolution of plant pathogenic fungi. Theory in classical population genetics is largely based on models that presume idealized, sexually reproducing populations of diploid species. These models usually do not apply accurately to the range of reproductive systems exhibited by plant pathog ens. Much work remains to make models that better

Gene Flow in Plant Pathosystems

Plant pathogens can emerge in agricultural ecosystems through several mechanisms, including host-tracking, host jumps, hybridization and horizontal gene transfer. High-throughput DNA sequencing coupled with new analytical approaches make it possible to differentiate among these mechanisms and to infer the time and place where pathogens first emerged. We present several examples to illustrate the different mechanisms and timescales associated with the origins of important plant pathogens. In some cases pathogens were domesticated along with their hosts during the invention of agriculture approximately 10,000 years ago. In other cases pathogens appear to have emerged very recently and almost instantaneously following horizontal gene transfer or hybridization. The predominant unifying feature in these examples is the environmental and genetic uniformity of the agricultural ecosystem in which the pathogens emerged. We conclude that agro-ecosystems will continue to select for new pathogens unless they are re-engineered to make them less conducive to pathogen emergence.

https://tarwi.lamolina.edu.pe/~fonz/pmdas/87.pdf

The Origins of Plant Pathogens in Agro-Ecosystems

The durability of disease resistance is affected by the evolutionary potential of the pathogen population Pathogens with a high evolutionary potential are more likely to overcome genetic resistance than pathogens with a low evolutionary potential We will propose a set of guidelines to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure Under our model of pathogen evolution, the two most important parameters to consider are reproduction/mating system and gene/genotype flow Pathogens that pose the greatest risk of breaking down resistance genes are those that possess a mixed reproduction system, with at least one sexual cycle per growing season and asexual reproduction during the epidemic phase, and a high potential for gene flow The lowest risk pathogens are those with strict asexual reproduction and low potential for gene flow We will present examples of high- and low-risk pathogens Knowledge of the population genetic structure of the pathogen may offer insight into the best breeding strategy for durable resistance We will present broad guidelines suggesting a rational method for breeding durable resistance according to the population genetics of the pathogen

Bruce A. McDonald

Papers

Pathogen population genetics, evolutionary potential, and durable resistance

Emergence of a new disease as a result of interspecific virulence gene transfer.

Gene Flow in Plant Pathosystems

The Origins of Plant Pathogens in Agro-Ecosystems

The population genetics of plant pathogens and breeding strategies for durable resistance