Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus
Marina Marcet-Houben,Ana-Rosa Ballester,Beatriz de la Fuente,Eleonora Harries,Jose F. Marcos,Luis González-Candelas,Toni Gabaldón +6 more
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TLDR
The complete genome of P. digitatum, the first of a phytopathogenic Penicillium species, is a valuable tool for understanding the virulence mechanisms and host-specificity of this economically important pest.Abstract:
Penicillium digitatum is a fungal necrotroph causing a common citrus postharvest disease known as green mold. In order to gain insight into the genetic bases of its virulence mechanisms and its high degree of host-specificity, the genomes of two P. digitatum strains that differ in their antifungal resistance traits have been sequenced and compared with those of 28 other Pezizomycotina. The two sequenced genomes are highly similar, but important differences between them include the presence of a unique gene cluster in the resistant strain, and mutations previously shown to confer fungicide resistance. The two strains, which were isolated in Spain, and another isolated in China have identical mitochondrial genome sequences suggesting a recent worldwide expansion of the species. Comparison with the closely-related but non-phytopathogenic P. chrysogenum reveals a much smaller gene content in P. digitatum, consistent with a more specialized lifestyle. We show that large regions of the P. chrysogenum genome, including entire supercontigs, are absent from P. digitatum, and that this is the result of large gene family expansions rather than acquisition through horizontal gene transfer. Our analysis of the P. digitatum genome is indicative of heterothallic sexual reproduction and reveals the molecular basis for the inability of this species to assimilate nitrate or produce the metabolites patulin and penicillin. Finally, we identify the predicted secretome, which provides a first approximation to the protein repertoire used during invasive growth. The complete genome of P. digitatum, the first of a phytopathogenic Penicillium species, is a valuable tool for understanding the virulence mechanisms and host-specificity of this economically important pest.read more
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Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
Ronald P. de Vries,Robert Riley,Ad Wiebenga,Guillermo Aguilar-Osorio,Sotiris Amillis,Cristiane Uchima,Gregor Anderluh,Mojtaba Asadollahi,Marion Askin,Marion Askin,Kerrie Barry,Evy Battaglia,Özgür Bayram,Özgür Bayram,Tiziano Benocci,Susanna A. Braus-Stromeyer,Camila Caldana,David Cánovas,David Cánovas,Gustavo C. Cerqueira,Fusheng Chen,Wanping Chen,Cindy Choi,Alicia Clum,Renato Augusto Corrêa dos Santos,André Damasio,George Diallinas,Tamás Emri,Erzsébet Fekete,Michel Flipphi,Susanne Freyberg,Antonia Gallo,Christos Gournas,Rob Habgood,Matthieu Hainaut,María Harispe,Bernard Henrissat,Bernard Henrissat,Bernard Henrissat,Kristiina Hildén,Ryan Hope,Abeer Hossain,Eugenia Karabika,Eugenia Karabika,Levente Karaffa,Zsolt Karányi,Nada Kraševec,Alan Kuo,Harald Kusch,Kurt LaButti,Ellen Lagendijk,Alla Lapidus,Alla Lapidus,Anthony Levasseur,Erika Lindquist,Anna Lipzen,Antonio F. Logrieco,Andrew MacCabe,Miia R. Mäkelä,Iran Malavazi,Petter Melin,Vera Meyer,Natalia Mielnichuk,Natalia Mielnichuk,Márton Miskei,Ákos Molnár,Giuseppina Mulè,Chew Yee Ngan,Margarita Orejas,Erzsébet Orosz,Erzsébet Orosz,Jean Paul Ouedraogo,Jean Paul Ouedraogo,Karin M. Overkamp,Hee-Soo Park,Giancarlo Perrone,François Piumi,François Piumi,Peter J. Punt,Arthur F. J. Ram,Ana Ramón,Stefan Rauscher,Eric Record,Diego Mauricio Riaño-Pachón,Vincent Robert,Julian Röhrig,Roberto Ruller,Asaf Salamov,Nadhira Salih,Nadhira Salih,Rob Samson,Erzsébet Sándor,Manuel Sanguinetti,Tabea Schütze,Tabea Schütze,Kristina Sepčić,Ekaterina Shelest,Gavin Sherlock,Vicky Sophianopoulou,Fabio M. Squina,Hui Sun,Antonia Susca,Richard B. Todd,Adrian Tsang,Shiela E. Unkles,Nathalie van de Wiele,Diana van Rossen-Uffink,Juliana Velasco de Castro Oliveira,Tammi Camilla Vesth,Jaap Visser,Jae-Hyuk Yu,Miaomiao Zhou,Mikael Rørdam Andersen,David B. Archer,Scott E. Baker,Isabelle Benoit,Isabelle Benoit,Axel A. Brakhage,Gerhard H. Braus,Reinhard Fischer,Jens Christian Frisvad,Gustavo H. Goldman,Jos Houbraken,Berl R. Oakley,István Pócsi,Claudio Scazzocchio,Claudio Scazzocchio,Bernhard Seiboth,Patricia A. vanKuyk,Patricia A. vanKuyk,Jennifer R. Wortman,Paul S. Dyer,Igor V. Grigoriev +132 more
TL;DR: In this article, a comparative genomics and experimental study of the aspergilli genus is presented, which allows for the first time a genus-wide view of the biological diversity of the Aspergillus and in many, but not all, cases linked genome differences to phenotype.
Journal ArticleDOI
EffectorP: predicting fungal effector proteins from secretomes using machine learning.
Jana Sperschneider,Donald M. Gardiner,Peter N. Dodds,Francesco Tini,Francesco Tini,Lorenzo Covarelli,Karam B. Singh,John M. Manners,Jennifer M. Taylor +8 more
TL;DR: EffectorP is the first prediction program for fungal effectors based on machine learning and will facilitate functionalfungal effector studies and improve the understanding of effectors in plant-pathogen interactions.
Journal ArticleDOI
Extracellular electron transfer systems fuel cellulose oxidative degradation.
Daniel Kracher,Stefan Scheiblbrandner,Alfons K. G. Felice,Erik Breslmayr,Marita Preims,Karolina Ludwicka,Karolina Ludwicka,Dietmar Haltrich,Vincent G. H. Eijsink,Roland Ludwig +9 more
TL;DR: Different extracellular electron sources for LPMOs are characterized and compared: cellobiose dehydrogenase, phenols procured from plant biomass or produced by fungi, and glucose-methanol-choline oxidoreductases that regenerate LPMO-reducing diphenols, demonstrating that all three are functional and that their relative importance during cellulose degradation depends on fungal lifestyle.
Journal ArticleDOI
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage.
TL;DR: This work used phylogenomics to study the ancient genome duplication occurred in the yeast Saccharomyces cerevisiae lineage and found compelling evidence for the existence of a contemporaneous interspecies hybridization.
Journal ArticleDOI
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.
Jaime Huerta-Cepas,Salvador Capella-Gutierrez,Leszek P. Pryszcz,Marina Marcet-Houben,Toni Gabaldón +4 more
TL;DR: A benchmark of the orthology predictions provided by the database is discussed, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes are discussed.
References
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Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Proceedings Article
Information Theory and an Extention of the Maximum Likelihood Principle
TL;DR: The classical maximum likelihood principle can be considered to be a method of asymptotic realization of an optimum estimate with respect to a very general information theoretic criterion to provide answers to many practical problems of statistical model fitting.
Book ChapterDOI
Information Theory and an Extension of the Maximum Likelihood Principle
TL;DR: In this paper, it is shown that the classical maximum likelihood principle can be considered to be a method of asymptotic realization of an optimum estimate with respect to a very general information theoretic criterion.
Journal ArticleDOI
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Stéphane Guindon,Jean-François Dufayard,Vincent Lefort,Maria Anisimova,Wim Hordijk,Olivier Gascuel +5 more
TL;DR: A new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves and a new test to assess the support of the data for internal branches of a phylogeny are introduced.
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