Fungal Genetic and Genomics
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Ten Simple Rules for Developing Usable Software in Computational Biology

Ten Simple Rules for Developing Usable Software in Computational Biology | Fungal Genetic and Genomics | Scoop.it
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Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L - Jeffries - 2016 - Molecular Ecology 

Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L - Jeffries - 2016 - Molecular Ecology  | Fungal Genetic and Genomics | Scoop.it
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BMC Bioinformatics

BMC Bioinformatics | Fungal Genetic and Genomics | Scoop.it

BMC Bioinformatics is an open access journal publishing original peer-reviewed research articles in all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. 
BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
BMC series - open, inclusive and trusted.

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The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities - Větrovský - 2015 - Molecular Ecology Resources - Wiley Online Library

The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities - Větrovský - 2015 - Molecular Ecology Resources - Wiley Online Library | Fungal Genetic and Genomics | Scoop.it
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Development of Fusarium graminearum perithecia in Maize Stalk Residues as Affected by Temperature and Moisture

Fusarium graminearum is the predominant component of the Fusarium head blight complex of wheat. F. graminearum ascospores, which initiate head infection, mature in perithecia on crop residues and become airborne. The effects of temperature (T) and moisture on perithecium production and maturation and on ascospore production on maize stalk residues were determined. In the laboratory, perithecia were produced at temperatures between 5 and 30°C (the optimum was 21.7°C), but matured only at 20 and 25°C. Perithecia were produced when relative humidity (RH) was ≥ 75% but matured only when RH was ≥ 85%; perithecium production and maturation increased with RH. Equations were developed describing perithecium production and maturation over time as a function of T and RH (R2 > 0.96). Maize stalks were also placed outdoors on three substrates: a grass lawn exposed to rain; a constantly wet, sponge-like foam exposed to rain; and a grass lawn protected from rain. No perithecia were produced on stalks protected from rain. Perithecia production and maturation were significantly higher on the constantly wet foam than on the intermittently wet lawn (both exposed to rain). Ascospore numbers but not their dispersal patterns were also affected by the substrate.
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mSystems - An Open-Access Journal Published by The American Society for Microbiology

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Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis : Nature Communications : Nature Publishing Group

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis : Nature Communications : Nature Publishing Group | Fungal Genetic and Genomics | Scoop.it
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should also work with fungal system with mixed fungal pathogen infection, and their potential for fungicide resistance.

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Below-ground plant–fungus network topology is not congruent with above-ground plant–animal network topology

Below-ground plant–fungus network topology is not congruent with above-ground plant–animal network topology | Fungal Genetic and Genomics | Scoop.it
In nature, plants and their pollinating and/or seed-dispersing animals form complex interaction networks. The commonly observed pattern of links between specialists and generalists in these networks has been predicted to promote species coexistence. Plants also build highly species-rich mutualistic networks below ground with root-associated fungi, and the structure of these plant–fungus networks may also affect terrestrial community processes. By compiling high-throughput DNA sequencing data sets of the symbiosis of plants and their root-associated fungi from three localities along a latitudinal gradient, we uncovered the entire network architecture of these interactions under contrasting environmental conditions. Each network included more than 30 plant species and hundreds of mycorrhizal and endophytic fungi belonging to diverse phylogenetic groups. The results were consistent with the notion that processes shaping host-plant specialization of fungal species generate a unique linkage pattern that strongly contrasts with the pattern of above-ground plant–partner networks. Specifically, plant–fungus networks lacked a “nested” architecture, which has been considered to promote species coexistence in plant–partner networks. Rather, the below-ground networks had a conspicuous “antinested” topology. Our findings lead to the working hypothesis that terrestrial plant community dynamics are likely determined by the balance between above-ground and below-ground webs of interspecific interactions.

Via Jean-Michel Ané, Steve Marek, Niklaus Grunwald
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On the occurrence of false positives in tests of migration under an isolation-with-migration model - Hey - 2015 - Molecular Ecology - Wiley Online Library

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Asexual sporulation facilitates adaptation: The emergence of azole resistance in Aspergillus fumigatus - Zhang - 2015 - Evolution - Wiley Online Library

asexual sporulation facilitates adaptation
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asexual sporulation facilitates adaptation

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Rescooped by Jie Wang from Plant Pathogenomics
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Frontiers: Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects (2015)

Frontiers: Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects (2015) | Fungal Genetic and Genomics | Scoop.it
The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.

Via Kamoun Lab @ TSL
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Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon - Schmidt - 2015 - New Phytologist - Wiley Online Library

(Fig.  2b). Candidate 1A is absent in Fom009 while FomSIX6 is absent in Fom010 and Fom009.
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Clonal reproduction in fungi

Clonal reproduction in fungi | Fungal Genetic and Genomics | Scoop.it

Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305–E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest.

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Belowground responses to elevation in a changing cloud forest - Looby - 2016 - Ecology and Evolution - Wiley Online Library

Belowground responses to elevation in a changing cloud forest - Looby - 2016 - Ecology and Evolution - Wiley Online Library | Fungal Genetic and Genomics | Scoop.it
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The program STRUCTURE does not reliably recover the correct population structure when sampling is uneven: sub-sampling and new estimators alleviate the problem - Puechmaille - Molecular Ecology Res...

The program STRUCTURE does not reliably recover the correct population structure when sampling is uneven: sub-sampling and new estimators alleviate the problem - Puechmaille - Molecular Ecology Res... | Fungal Genetic and Genomics | Scoop.it
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DNA barcodes from century-old type specimens using next-generation sequencing - Prosser - 2015 - Molecular Ecology Resources - Wiley Online Library

DNA barcodes from century-old type specimens using next-generation sequencing - Prosser - 2015 - Molecular Ecology Resources - Wiley Online Library | Fungal Genetic and Genomics | Scoop.it
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A note on the use of multiple linear regression in molecular ecology - Frasier - 2015 - Molecular Ecology Resources - Wiley Online Library

A note on the use of multiple linear regression in molecular ecology - Frasier - 2015 - Molecular Ecology Resources - Wiley Online Library | Fungal Genetic and Genomics | Scoop.it
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Rescooped by Jie Wang from MycorWeb Plant-Microbe Interactions
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β-glucan: Crucial component of the fungal cell wall and elusive MAMP in plants

β-glucan: Crucial component of the fungal cell wall and elusive MAMP in plants | Fungal Genetic and Genomics | Scoop.it

Plant innate immunity relies in first place on the detection of invading microbes. Thus, plants evolved receptors to sense unique molecules of the microbe, the so called microbe-associated molecular patterns or MAMPs. The best studied fungal MAMP is chitin, an important structural building block of the fungal cell wall. Over the past years several plant receptors for chitin have been characterized as well as different strategies adopted by fungi to evade chitin recognition. Despite its strong activity as an elicitor of plant defense chitin represents only a small percentage of the cell wall of most fungi compared to other complex sugars. β-glucan, the most abundant fungal cell wall polysaccharide, also serves as a MAMP, but the mechanisms of β-glucan perception and signaling in plants are largely unknown. In contrast to that the β-glucan recognition and signaling machineries are well characterized in mammals. The C-type lectin receptor Dectin-1 is a key component of these machineries. In this review we describe valuable knowledge about the existence of at least one β-glucan receptor in plants and about the hindrances in β-glucan research. Additionally we discuss possible future perspectives of glucan research and the possibility to transfer the gathered knowledge from mammalian systems to plants.


Via Francis Martin
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Low multifunctional redundancy of soil fungal diversity at multiple scales - Mori - 2015 - Ecology Letters - Wiley Online Library

Low multifunctional redundancy of soil fungal diversity at multiple scales - Mori - 2015 - Ecology Letters - Wiley Online Library | Fungal Genetic and Genomics | Scoop.it
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Efficient disruption and replacement of an effector gene in the oomycete Phytophthora sojae using CRISPR/Cas9 - Fang - 2015 - Molecular Plant Pathology - Wiley Online Library

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Phenotypic and genotypic variation in Michigan populations of Phytophthora infestans from 2008 to 2010 - Rojas - Plant Pathology - Wiley Online Library

Phenotypic and genotypic variation in Michigan populations of Phytophthora infestans from 2008 to 2010 - Rojas - Plant Pathology - Wiley Online Library | Fungal Genetic and Genomics | Scoop.it
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@Alejandro Rojas's New Paper!

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Genes are information, so information theory is coming to the aid of evolutionary biology - Sherwin - 2015 - Molecular Ecology Resources - Wiley Online Library

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Information theory in Evolution biology

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Adaptations: Using Darwin's Origin to teach biology and writing - Morris - 2015 - Evolution - Wiley Online Library

Adaptations: Using Darwin's Origin to teach biology and writing - Morris - 2015 - Evolution - Wiley Online Library | Fungal Genetic and Genomics | Scoop.it
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Does the P value have a future in plant pathology? — Phytopathology

Does the P value have a future in plant pathology? — Phytopathology | Fungal Genetic and Genomics | Scoop.it
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.05 || .01

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The advantage of short paper titles

The advantage of short paper titles | Fungal Genetic and Genomics | Scoop.it
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Papers with shorter titles get more citations
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