Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
Robin A. Ohm,Nicolas Feau,Bernard Henrissat,Conrad L. Schoch,Benjamin A. Horwitz,Kerrie Barry,Bradford Condon,Alex Copeland,Braham Dhillon,Fabian Glaser,Cedar N. Hesse,Idit Kosti,Kurt LaButti,Erika Lindquist,Susan Lucas,Asaf Salamov,Rosie E. Bradshaw,Lynda M. Ciuffetti,Richard C. Hamelin,Richard C. Hamelin,Gert H. J. Kema,Christopher B. Lawrence,James A. Scott,Joseph W. Spatafora,B. Gillian Turgeon,Pierre J. G. M. de Wit,Shaobin Zhong,Stephen B. Goodwin,Igor V. Grigoriev +28 more
TLDR
The Dothideomycetes are one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts as mentioned in this paper.Abstract:
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.read more
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The carbohydrate-active enzymes database (CAZy) in 2013
TL;DR: The changes that have occurred in CAZy during the past 5 years are outlined and a novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes is presented.
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MycoCosm portal: gearing up for 1000 fungal genomes
Igor V. Grigoriev,Roman Nikitin,Sajeet Haridas,Alan Kuo,Robin A. Ohm,Robert Otillar,Robert Riley,Asaf Salamov,Xueling Zhao,Frank Korzeniewski,Tatyana Smirnova,Henrik P. Nordberg,Inna Dubchak,Igor Shabalov +13 more
TL;DR: MycoCosm is a fungal genomics portal developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences and other 'omics' data by providing interactive web-based tools.
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Fungal Effectors and Plant Susceptibility
Libera Lo Presti,Daniel Lanver,Gabriel Schweizer,Shigeyuki Tanaka,Liang Liang,Marie Tollot,Alga Zuccaro,Stefanie Reissmann,Regine Kahmann +8 more
TL;DR: This review describes the effector repertoires of 84 plant-colonizing fungi and focuses on the mechanisms that allow these fungal effectors to promote virulence or compatibility, discuss common plant nodes that are targeted by effectors, and provide recent insights into effector evolution.
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Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3
TL;DR: The results show that errors in genome annotation do lead to higher inferred rates of gene gain and loss but that CAFE 3 sufficiently accounts for these errors to provide accurate estimates of important evolutionary parameters.
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