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      Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

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          Abstract

          Background

          Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei ( Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley ( Hordeum vulgare).

          Results

          The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes ( SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome.

          Conclusions

          The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a “one-speed” genome that differs in its architecture and (co-)evolutionary pattern from the “two-speed” genomes reported for several other filamentous phytopathogens.

          Electronic supplementary material

          The online version of this article (10.1186/s12864-018-4750-6) contains supplementary material, which is available to authorized users.

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          Most cited references 54

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          featureCounts: An efficient general-purpose program for assigning sequence reads to genomic features

           ,  ,   (2013)
          Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.
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            Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.

            We describe a new ab initio algorithm, GeneMark-ES version 2, that identifies protein-coding genes in fungal genomes. The algorithm does not require a predetermined training set to estimate parameters of the underlying hidden Markov model (HMM). Instead, the anonymous genomic sequence in question is used as an input for iterative unsupervised training. The algorithm extends our previously developed method tested on genomes of Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster. To better reflect features of fungal gene organization, we enhanced the intron submodel to accommodate sequences with and without branch point sites. This design enables the algorithm to work equally well for species with the kinds of variations in splicing mechanisms seen in the fungal phyla Ascomycota, Basidiomycota, and Zygomycota. Upon self-training, the intron submodel switches on in several steps to reach its full complexity. We demonstrate that the algorithm accuracy, both at the exon and the whole gene level, is favorably compared to the accuracy of gene finders that employ supervised training. Application of the new method to known fungal genomes indicates substantial improvement over existing annotations. By eliminating the effort necessary to build comprehensive training sets, the new algorithm can streamline and accelerate the process of annotation in a large number of fungal genome sequencing projects.
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              Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism.

              Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.
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                Author and article information

                Contributors
                lamprinos.frantzeskakis@rwth-aachen.de
                kracher@mpipz.mpg.de
                skusch@bio1.rwth-aachen.de
                makoto@mpipz.mpg.de
                sbauer@mpipz.mpg.de
                cpr@plen.ku.dk
                p.spanu@imperial.ac.uk
                maekawa@mpipz.mpg.de
                schlef@mpipz.mpg.de
                panstruga@bio1.rwth-aachen.de
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                22 May 2018
                22 May 2018
                2018
                : 19
                Affiliations
                [1 ]ISNI 0000 0001 0728 696X, GRID grid.1957.a, Institute for Biology I, Unit of Plant Molecular Cell Biology, , RWTH Aachen University, ; Worringerweg 1, 52056 Aachen, Germany
                [2 ]ISNI 0000 0001 0660 6765, GRID grid.419498.9, Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, ; Carl-von-Linné-Weg 10, 50829 Cologne, Germany
                [3 ]ISNI 0000 0001 0674 042X, GRID grid.5254.6, Department of Plant and Environmental Sciences, , University of Copenhagen, ; Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
                [4 ]ISNI 0000 0001 2113 8111, GRID grid.7445.2, Imperial College, Department of Life Sciences, ; Sir Alexander Fleming Building, London, SW7 2AZ UK
                Article
                4750
                10.1186/s12864-018-4750-6
                5964911
                29788921
                © The Author(s). 2018

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;
                Award ID: SPP1819 (PA 861/14-1)
                Award ID: SFB670/3 (grant #13123509)
                Award Recipient :
                Funded by: Strategiske Forskningsråd (DK)
                Award ID: 10-093504
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2018

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