The Promise and Pitfalls of Sequence-Based Identification of Plant-Pathogenic Fungi and Oomycetes

Sequences of selected marker loci have been widely used for the identification of specific pathogens and the development of sequence-based diagnostic methods. Although such approaches offer several advantages over traditional culture-based methods for pathogen diagnosis and identification, they have their own pitfalls. These include erroneous and incomplete data in reference databases, poor or oversimplified interpretation of search results, and problems associated with defining species boundaries. In this letter, we outline the potential benefits and drawbacks of using sequence data for identification and taxonomic deductions of plant-pathogenic fungi and oomycetes, using Phytophthora as a primary example. We also discuss potential remedies for these pitfalls and address why coordinated community efforts are essential to make such remedies more efficient and robust.

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Species boundaries in plant pathogenic fungi: a Colletotrichum case study

BMC Evolutionary Biology ◽

10.1186/s12862-016-0649-5 ◽

2016 ◽

Vol 16 (1) ◽

Cited By ~ 55

Author(s):

Fang Liu ◽

Mei Wang ◽

Ulrike Damm ◽

Pedro W. Crous ◽

Lei Cai

Keyword(s):

Pathogenic Fungi ◽

Species Boundaries ◽

Plant Pathogenic Fungi

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Plant Pathogenic Fungi Associated with Coraebus florentinus (Coleoptera: Buprestidae) Attacks in Declining Oak Forests

Forests ◽

10.3390/f10060488 ◽

2019 ◽

Vol 10 (6) ◽

pp. 488 ◽

Cited By ~ 2

Author(s):

Claudia Pinna ◽

Benedetto T. Linaldeddu ◽

Vitale Deiana ◽

Lucia Maddau ◽

Lucio Montecchio ◽

...

Keyword(s):

Sequence Data ◽

Management Strategies ◽

Pathogenic Fungi ◽

Fungal Species ◽

Western Mediterranean ◽

Plant Pathogenic Fungi ◽

Limited Information ◽

Natural Ecosystems ◽

Oak Trees ◽

Coraebus Florentinus

The black-banded oak borer, Coraebus florentinus, is an emerging pest of oak trees in the western Mediterranean region. Larvae of the insect are xylophagous and progressively excavate an annular gallery that interrupts sap flow, resulting in the death of the attacked branches. Until now, limited information has been available regarding the ecological interactions between C. florentinus and the main plant pathogenic fungi involved in the etiology of oak decline. Knowledge of these interactions is important in understanding their impact in natural ecosystems and developing appropriate management strategies. Therefore, in this study, we characterized the fungal communities occurring in the exoskeleton of adults and larvae of C. florentinus and associated with the necrotic wood tissues surrounding the branch galleries of declining oak trees. A total of 29 fungal species were identified based on DNA sequence data and morphological features, of which 14 were from symptomatic woody tissues, six from insect exoskeleton, and nine from both insects and symptomatic wood tissues. The most frequent fungal species, Cryphonectria naterciae (15.9% of isolates), Dothiorella iberica (11.3%), and Diplodia corticola (9.9%), were isolated from both insect and gallery systems. All three species are well-known oak pathogens and are reported here, for the first time, to be associated with C. florentinus. At the same time, 89.6% of the fungal taxa were isolated from one or two sites, highlighting the site-dependence of fungal community assemblages.

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Phylogeny and species delimitations in the entomopathogenic genus Beauveria (Hypocreales, Ascomycota), including the description of B. peruviensis sp. nov.

MycoKeys ◽

10.3897/mycokeys.58.35764 ◽

2019 ◽

Vol 58 ◽

pp. 47-68 ◽

Cited By ~ 5

Author(s):

Danilo E. Bustamante ◽

Manuel Oliva ◽

Santos Leiva ◽

Jani E. Mendoza ◽

Leidy Bobadilla ◽

...

Keyword(s):

Genetic Distance ◽

Sequence Data ◽

Pathogenic Fungi ◽

Species Boundaries ◽

New Taxon ◽

Important Species ◽

Genealogical Concordance ◽

Structural Simplicity ◽

Molecular Makers ◽

Multilocus Phylogeny

The genus Beauveria is considered a cosmopolitan anamorphic and teleomorphic genus of soilborne necrotrophic arthropod-pathogenic fungi that includes ecologically and economically important species. Species identification in Beauveria is difficult because of its structural simplicity and the lack of distinctive phenotypic variation. Therefore, the use of multi-locus sequence data is essential to establish robust species boundaries in addition to DNA-based species delimitation methods using genetic distance, coalescent, and genealogical concordance approaches (polyphasic approaches). In this regard, our study used multilocus phylogeny and five DNA-based methods to delimit species in Beauveria using three molecular makers. These polyphasic analyses allowed for the delimitation of 20–28 species in Beauveria, confirming cryptic diversity in five species (i.e. B. amorpha, B. bassiana, B. diapheromeriphila, and B. pseudobassiana) and supporting the description of B. peruviensis as a new taxon from northeastern Peru. The other five species were not evaluated as they did not have enough data (i.e. B. araneola, B. gryllotalpidicola, B. loeiensis, B. medogensis, and B. rudraprayagi). Our results demonstrate that the congruence among different methods in a polyphasic approach (e.g. genetic distance and coalescence methods) is more likely to show reliably supported species boundaries. Among the methods applied in this study, genetic distance, coalescent approaches, and multilocus phylogeny are crucial when establishing species boundaries in Beauveria.

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Improving ITS sequence data for identification of plant pathogenic fungi

Fungal Diversity ◽

10.1007/s13225-014-0291-8 ◽

2014 ◽

Vol 67 (1) ◽

pp. 11-19 ◽

Cited By ~ 81

Author(s):

R. Henrik Nilsson ◽

Kevin D. Hyde ◽

Julia Pawłowska ◽

Martin Ryberg ◽

Leho Tedersoo ◽

...

Keyword(s):

Sequence Data ◽

Pathogenic Fungi ◽

Its Sequence ◽

Plant Pathogenic Fungi

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Development of genome editing technologies for plant pathogenic fungi

Japanese Journal of Phytopathology ◽

10.3186/jjphytopath.86.264 ◽

2020 ◽

Vol 86 (4) ◽

pp. 264

Author(s):

T. ARAZOE

Keyword(s):

Genome Editing ◽

Pathogenic Fungi ◽

Plant Pathogenic Fungi

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Comparative Fungicidal Activity of some Pure and Nanoemulsion Monoterpenes Effects on Soil Borne Plant Pathogenic Fungi

Journal of Plant Protection and Pathology ◽

10.21608/jppp.2018.43962 ◽

2018 ◽

Vol 9 (10) ◽

pp. 707-713

Author(s):

Mona Abdelrasoul ◽

G. Amer

Keyword(s):

Fungicidal Activity ◽

Pathogenic Fungi ◽

Plant Pathogenic Fungi

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Fungal Phytotoxins in Sustainable Weed Management

Current Medicinal Chemistry ◽

10.2174/0929867324666170426152331 ◽

2018 ◽

Vol 25 (2) ◽

pp. 268-286 ◽

Cited By ~ 4

Author(s):

Maurizio Vurro ◽

Angela Boari ◽

Francesca Casella ◽

Maria Chiara Zonno

Keyword(s):

Weed Management ◽

Pathogenic Fungi ◽

Mechanisms Of Action ◽

Limiting Factors ◽

Integrated Weed Management ◽

Plant Pathogenic Fungi ◽

Design Strategies ◽

Disease Etiology ◽

Chemical Structures ◽

Toxic Metabolites

Fungal phytotoxins are natural secondary metabolites produced by plant pathogenic fungi during host–pathogen interactions. They have received considerable particular attention for elucidating disease etiology, and consequently to design strategies for disease control. Due to wide differences in their chemical structures, these toxic metabolites have different ecological and environmental roles and mechanisms of action. This review aims at summarizing the studies on the possible use of these metabolites as tools in biological and integrated weed management, e.g. as: novel and environmentally friendly herbicides; lead for novel compounds; sources of novel mechanisms of action. Moreover, the limiting factors for utilizing those metabolites in practice will also be briefly discussed.

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First record of Pestalotiopsis spp. from affected leaves of mastic shrubs (Pestacia lentiscus L.) in northeastern of Libya.

International Journal of Bioassays ◽

10.21746/ijbio.2016.08.004 ◽

2016 ◽

Vol 5 (08) ◽

pp. 4744

Author(s):

Zahra Ibrahim El-Gali

Keyword(s):

Signs And Symptoms ◽

Pathogenic Fungi ◽

First Record ◽

Plant Pathogenic Fungi ◽

Pistacia Lentiscus ◽

Plant Materials ◽

Al Jabal Al Akhdar ◽

First Time

This study was carried out to identify the unknown different symptoms and their causes as plant pathogenic fungi from Al-Jabal Al-Akhdar District. Plant materials with fungal signs and symptoms were collected and examined. The main fungi consistently isolated from symptomatic leaves and twigs were Pestalotiopsis spp. Morphology, colony characteristics, and pathogenicity of the isolates were examined. My report the occurrence of Pestalotiopsis spp. on leaves of mastic (Pistacia lentiscus) for the first time in Libya.

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