Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata

The Venturia genus comprises fungal species that are pathogens on Rosaceae host plants, including V. inaequalis and V. asperata on apple, V. aucupariae on sorbus and V. pirina on pear. Although the genetic structure of V. inaequalis populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87 Venturia strains that represent each species and each population within V. inaequalis. We present a PacBio genome assembly for the V. inaequalis EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of V. inaequalis and V. aucupariae contain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly of V. inaequalis presents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research of Venturia pathogens. Especially, it will help understanding the evolutionary history of Venturia species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.

[1]  Xiang-ming Xu,et al.  Annotated Draft Genome Sequence of the Apple Scab Pathogen Venturia inaequalis , 2018, Microbiology Resource Announcements.

[2]  K. Plummer,et al.  Evidence for Sexual Reproduction: Identification, Frequency, and Spatial Distribution of Venturia effusa (Pecan Scab) Mating Type Idiomorphs. , 2018, Phytopathology.

[3]  Andrew J. Robinson,et al.  Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range , 2017, BMC Genomics.

[4]  N. Baisakh,et al.  Population Genetic Structure of Apple Scab (Venturia inaequalis (Cooke) G. Winter) in Iran , 2016, PloS one.

[5]  F. Yu,et al.  Draft genome sequence of Fusicladium effusum, cause of pecan scab , 2016, Standards in genomic sciences.

[6]  James K. Hane,et al.  OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes , 2016, Genome biology and evolution.

[7]  J. Celton,et al.  When virulence originates from nonagricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts in Venturia inaequalis. , 2016, The New phytologist.

[8]  P. Gladieux,et al.  Emergence of new virulent populations of apple scab from nonagricultural disease reservoirs. , 2016, The New phytologist.

[9]  Andrew J. Robinson,et al.  A Large Family of AvrLm6-like Genes in the Apple and Pear Scab Pathogens, Venturia inaequalis and Venturia pirina , 2015, Front. Plant Sci..

[10]  Christine Tranchant-Dubreuil,et al.  TOGGLE: toolbox for generic NGS analyses , 2015, BMC Bioinformatics.

[11]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[12]  S. Reissmann,et al.  Fungal effectors and plant susceptibility. , 2015, Annual review of plant biology.

[13]  Katharina J. Hoff,et al.  BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS , 2016, Bioinform..

[14]  J. Landolin,et al.  Assembling large genomes with single-molecule sequencing and locality-sensitive hashing , 2014, Nature Biotechnology.

[15]  S. Mathivanan,et al.  Proteogenomic analysis of the Venturia pirina (Pear Scab Fungus) secretome reveals potential effectors. , 2014, Journal of proteome research.

[16]  H. Quesneville,et al.  PASTEC: An Automatic Transposable Element Classification Tool , 2014, PloS one.

[17]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[18]  P. Renault,et al.  Multiple recent horizontal transfers of a large genomic region in cheese making fungi , 2014, Nature Communications.

[19]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[20]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[21]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[22]  B. Le Cam,et al.  The genetic structure of a Venturia inaequalis population in a heterogeneous host population composed of different Malus species , 2013, BMC Evolutionary Biology.

[23]  David W. Cheung,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[24]  M. Schmitz,et al.  Structure, dynamics and domain organization of the repeat protein Cin1 from the apple scab fungus. , 2012, Biochimica et biophysica acta.

[25]  M. Chevalier,et al.  A new scab-like disease on apple caused by the formerly saprotrophic fungus Venturia asperata , 2012 .

[26]  H. Swerdlow,et al.  A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers , 2012, BMC Genomics.

[27]  D. Kwiatkowski,et al.  Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes , 2012, BMC Genomics.

[28]  K. Hyde,et al.  A molecular, morphological and ecological re-appraisal of Venturiales―a new order of Dothideomycetes , 2011, Fungal Diversity.

[29]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[30]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[31]  Martin Goodson,et al.  Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. , 2011, Genome research.

[32]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[33]  T. Fennell,et al.  Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries , 2011, Genome Biology.

[34]  Jean,et al.  Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations , 2011, Nature communications.

[35]  V. Bus,et al.  Venturia inaequalis: the causal agent of apple scab. , 2011, Molecular plant pathology.

[36]  T. Flutre,et al.  Considering Transposable Element Diversification in De Novo Annotation Approaches , 2011, PloS one.

[37]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[38]  P. Gladieux,et al.  Host-specific differentiation among populations of Venturia inaequalis causing scab on apple, pyracantha and loquat. , 2010, Fungal genetics and biology : FG & B.

[39]  I. Roldán‐Ruiz,et al.  Evolution of the population structure of Venturia inaequalis, the apple scab fungus, associated with the domestication of its host , 2010, Molecular ecology.

[40]  W. Cui,et al.  Candidate effector gene identification in the ascomycete fungal phytopathogen Venturia inaequalis by expressed sequence tag analysis. , 2009, Molecular plant pathology.

[41]  K. Plummer,et al.  Two novel Venturia inaequalis genes induced upon morphogenetic differentiation during infection and in vitro growth on cellophane. , 2008, Fungal genetics and biology : FG & B.

[42]  Pier Luigi Martelli,et al.  PredGPI: a GPI-anchor predictor , 2008, BMC Bioinformatics.

[43]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[44]  David Haussler,et al.  Using native and syntenically mapped cDNA alignments to improve de novo gene finding , 2008, Bioinform..

[45]  Pierre Gladieux,et al.  On the Origin and Spread of the Scab Disease of Apple: Out of Central Asia , 2008, PloS one.

[46]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[47]  U. Steiner,et al.  Localized Melanization of Appressoria Is Required for Pathogenicity of Venturia inaequalis. , 2007, Phytopathology.

[48]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[49]  P. Gladieux,et al.  Origin and colonization history of newly virulent strains of the phytopathogenic fungus Venturia inaequalis. , 2007, Fungal genetics and biology : FG & B.

[50]  Casey M. Bergman,et al.  Combined Evidence Annotation of Transposable Elements in Genome Sequences , 2005, PLoS Comput. Biol..

[51]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[52]  K. Schubert,et al.  Phylogenetic relationships of the anamorphic genus Fusicladium s. lat. as inferred by ITS nrDNA data , 2005, Mycological Progress.

[53]  F. Eisenhaber,et al.  A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe. , 2004, Journal of molecular biology.

[54]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[55]  J. Doležel,et al.  Nuclear DNA content and genome size of trout and human. , 2003, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[56]  S. Eddy,et al.  Automated de novo identification of repeat sequence families in sequenced genomes. , 2002, Genome research.

[57]  B. Le Cam,et al.  Evidence of Two Formae Speciales in Venturia inaequalis, Responsible for Apple and Pyracantha Scab. , 2002, Phytopathology.

[58]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[59]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[60]  L. Parisi,et al.  Genetics of Host-Pathogen Relationships Between Venturia inaequalis Races 6 and 7 and Malus Species. , 2000, Phytopathology.

[61]  E. Selker,et al.  Action of repeat-induced point mutation on both strands of a duplex and on tandem duplications of various sizes in Neurospora. , 1999, Genetics.

[62]  X. Huang,et al.  On global sequence alignment , 1994, Comput. Appl. Biosci..

[63]  H. Sandermann,et al.  A simple and efficient protocol for isolation of high molecular weight DNA from filamentous fungi, fruit bodies, and infected plant tissues. , 1992, Nucleic acids research.

[64]  Herb S. Aldwinckle,et al.  compendium of apple and pear diseases , 1990 .

[65]  A. Sivanesan.  The taxonomy and pathology of Venturia species , 1978 .

[66]  G. Samuels,et al.  Venturia asperata sp. nov. and its Fusicladium State on Apple Leaves , 1975 .

[67]  K. Schubert,et al.  Opportunistic, human-pathogenic species in the Herpotrichiellaceae are phenotypically similar to saprobic or phytopathogenic species in the Venturiaceae , 2007, Studies in mycology.

[68]  Eugene W. Myers,et al.  PILER : identification and classification of genomic repeats , 2005 .

[69]  M. Piotrowski,et al.  Purification and Partial Characterization of an Extracellular Melanoprotein from the Fungus Venturia inaequalis , 2005, Zeitschrift fur Naturforschung. C, Journal of biosciences.

[70]  H. Quesneville,et al.  Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes , 2003, Journal of Molecular Evolution.

[71]  R. Lewontin,et al.  Genetics and Biology , 1999 .

[72]  D. Marie,et al.  A cytometric exercise in plant DNA histograms, with 2C values for 70 species , 1993, Biology of the cell.