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    The Genomics of Powdery MildewFungi: Past Achievements, PresentStatus and Future ProspectsStphane Hacquard1Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne,Germany1Corresponding author: e-mail address: [email protected]


    1. General Introduction 1102. Biology of Powdery Mildew Infection 111

    2.1 Introduction 1112.2 Phylogeny 1112.3 Lifecycle and infection strategy 112

    3. Genomic Insights into the Obligate Biotrophic Lifestyle 1133.1 Introduction 1133.2 Genome-size expansion 1133.3 Transposable elements proliferation 1173.4 Gene family contraction 1183.5 Missing genes and pathways 119

    4. Comparative Genomics of Powdery Mildew Isolates: Insights into TheirReproductive Mode and Their Evolutionary Origin 1214.1 Introduction 1214.2 Mosaic genome structure 1214.3 Importance of clonal propagation 1234.4 Evolutionary origin 124

    5. Powdery Mildew Effector Research in the Genomic Area 1245.1 Introduction 1245.2 Prediction and variation of CSEP repertoires 1255.3 Evolution of CSEPs 1275.4 Structural features of CSEPs 1285.5 Functional analysis of CSEPs 129

    6. Transcriptomics of Powdery Mildew Fungi 1306.1 Introduction 1306.2 Haustorial transcriptome 1316.3 Transcript profiling during host infection 131

    7. Future Challenges in Powdery Mildew Research 133Acknowledgements 136References 136

    Advances in Botanical Research, Volume 70 # 2014 Elsevier LtdISSN 0065-2296 All rights reserved.


  • Abstract

    Powdery mildew fungi (Ascomycota phylum) are obligate biotrophic plant pathogensthat can only grow and reproduce on living host cells. They infect a wide range of plants,including many crops and the diseases they cause are common, easily recognizableand widespread. Although functional investigations in these genetically intractableorganisms have been hampered by their obligate biotrophic nature, recent advancesin genomics and transcriptomics have contributed tremendously to our understandingof powdery mildew biology. Comparative genomics was a powerful tool to pinpointwhat distinguishes powdery mildew fungi from other filamentous plant pathogensand helped us to better understand how obligate biotrophy evolved. Comparativegenome analyses among isolates in both the wheat and the barley powdery mildewlineages revealed isolate-specific mosaic genome structures of evolutionary youngand old haplogroups. In addition to providing hints into the evolutionary origin of pow-dery mildew fungi, the observed mosaic genome structure also reflects the reproduc-tive mode of these pathogens and explains how the large standing genetic variation isgenerated in powdery mildew populations. In this chapter, I discuss how the revolutionin genomics has contributed and will contribute in the future to better understand theobligate biotrophic lifestyle, the virulence arsenal, the reproductive mode and the evo-lutionary history of powdery mildew fungi.


    During the last decade, innovations in genomic technologies have

    revolutionized the research in the field of plantmicrobes interactions.

    The publication of the complete genome sequence of the first plant patho-

    genic fungus in 2005 (Dean et al., 2005) paved the way for the exponential

    increase of fungal and oomycete genome sequencing projects (Grigoriev

    et al., 2014; Pais et al., 2013). To date, dozens of genomes of filamentous

    plant pathogens have been sequenced, and ambitious projects have emerged

    such as the 1000 Fungal Genomes Project that aims to fill in the gaps in the

    fungal tree of life by sequencing at least two reference genomes from every

    known fungal family (; Grigoriev

    et al., 2014). Next-generation genome sequencing also had a tremendous

    impact on the study of noncultivable and genetically intractable organisms

    like powdery mildew fungi. In this chapter, I describe how genome

    sequencing of powdery mildew fungi has changed the way we conduct

    research and has contributed to better understand their evolution, their

    reproduction and their biology. I further discuss the future challenges in

    powdery mildew genomics and in powdery mildew research in general.

    110 Stphane Hacquard


    2.1. IntroductionPowdery mildew fungi are widespread plant pathogens that can infect more

    than 10,000 plant species including major cereals such as wheat and barley,

    vegetable crops such as tomato and cucurbits and ornamental species like

    roses (Glawe, 2008). The diseases they cause are also common on fruits

    and are characterized by easily recognizable patches of white to greyish,

    talcum powderlike growth. They have a significant impact on plant growth

    and yield quality. For instance, a reduction of up to 20% in grain yield has been

    observed in wheat fields in which susceptible cultivars severely infected by

    Blumeria graminis were grown (Conner, Kuzyk, & Su, 2003). Most powdery

    mildew species are host-specific or only able to infect a narrow host range,

    suggesting that their corresponding genomes encode distinct toolboxes

    of pathogenesis-associated genes (Schulze-Lefert & Panstruga, 2011). Impor-

    tantly, all powdery mildews are obligate biotrophs, meaning that they cannot

    be cultivated outside their hosts. Hence, they are entirely dependent on water

    and nutrients supply from living host cells for their growth and reproduction

    (Panstruga, 2003).

    2.2. PhylogenyPowdery mildew fungi belong to the Erysiphales order of the Ascomycota

    phylum. The Erysiphales belong to the Leotiomycetes class (Wang et al.,

    2006), in which many fungal pathogens causing serious plant disease are

    found, including many necrotrophic fungal pathogens that have very con-

    trasted host range and infection strategies compared with powdery mildew

    fungi (Amselem et al., 2011). To date, sixteen genera containing 900 spe-cies have been described in the Erysiphales order (Braun & Cook, 2012).

    While 12 genera (including Blumeria, Erysiphe and Golovinomyces) are ecto-

    parasites that produce vegetative mycelium and conidiospores epiphytically

    on the host surface, four genera are endoparasites that produce internal

    mycelia (Takamatsu, 2013). Only powdery mildew fungi belonging to

    the Leveillula genus produce true endophytic hyphae from which con-

    idiospores arise and emerge through stomata (Takamatsu, 2013). Molecular

    phylogenetic analyses, based on the amplification and the sequencing of the

    ribosomal DNA and the internal transcribed spacer regions, indicate that

    powdery mildew fungi form a monophyletic group (Mori, Sato, &

    111The Genomics of Powdery Mildew Fungi

  • Takamatsu, 2000; Wang et al., 2006). Therefore, the obligate biotrophic

    lifestyle of these pathogens may has arisen only once in their ancestry and

    has been further retained over evolutionary time.

    2.3. Lifecycle and infection strategyInfection by powdery mildew pathogens is initiated when an airborne asco-

    spore (sexual spore) lands on a susceptible host plant. For most powdery mil-

    dew fungi, the ascospore germinates and differentiates a hypha that elongates

    to produce a swollen appressorium from which a penetration peg emerged.

    The penetration peg punctures the host surface using a combination of

    mechanical force and enzymatic degradation (Howard, 1997; Pryce-

    Jones, Carver, & Gurr, 1999) and differentiates a haustorium that remains

    separated from the host cytoplasm by the host plasma membrane (Micali,

    Neumann, Grunewald, Panstruga, & OConnell, 2011; Szabo &

    Bushnell, 2001). The haustorium is a highly specialized structure that plays

    a central role in establishing and maintaining the intimate relationship with

    the host (Panstruga, 2003). In addition to its role in host nutrient uptake, the

    haustorium is also a platform for the secretion of small effector molecules that

    manipulate the host cell, thereby facilitating fungal colonization

    (Panstruga & Dodds, 2009). Once a successful interaction is established, sec-

    ondary haustoria are formed and vegetative hyphae are produced epiphyt-

    ically. Only few days after infection, conidiophores arise from the vegetative

    mycelium and produce large amounts of conidia (asexual spores) that are dis-

    seminated by winds to reinfect susceptible hosts (Glawe, 2008). Notably,

    germination of B. graminis conidia on ryegrass is triggered by C26 aldehydes,

    indicating that powdery mildew pathogens need chemical cues in epicutic-

    ular wax for germination (Ringelmann, Riedel, Riederer, & Hildebrandt,

    2009). The polycyclic asexual development of powdery mildew fungi

    and their rapid generation time (time from spore germination to spore pro-

    duction) lead to epidemics that gradually build up over spring and summer

    seasons. The obligate biotrophic lifestyle of powdery mildew fungi implies

    that they must be able to survive on their hosts throughout seasons. In

    Europe, the continuity of autumn- and spring-sown crops provides a

    green bridge for the fungus, allowing an unbroken asexual cycle across

    seasons when the weather conditions are favourable (Wolfe &

    McDermott, 1994). Sexual reproduction can also occurs at the end of the

    growing season of the host plant, when compatib