Special Issue "Detection and Diagnostics of Fungal and Oomycete Plant Pathogens"
Deadline for manuscript submissions: 30 November 2020.
Interests: technologies for detection and identification of plant pests (fungi-oomycetes) of regulatory significance; fungal detection and genotyping; phytophthora; Verticillium; real-time PCR; genomic; metagenomic
In agriculture and forestry the development and validation of molecular detection tools for different organisms is important for phytosanitary export certification, which relies on having methods to identify plant pathogens associated with plants, grains and seeds. To develop detection–identification assays, DNA sequence information and genomic resources are important. Over the last decade, several genomes of plant pathogens have been made available, largely due to the development of high-throughput sequencing (HTS) technologies that have enabled lower costs for sequencing genomes and the acquisition of data conducive to running metagenomic analyses. Knowledge of the genome and its structure can help us better understand these organisms and is a valuable resource for the development of detection and genotyping tools. Often disease may be present in plants despite no symptoms being visible. This underscores the importance of having molecular methods for the detection of pathogens for improved sensitivity and to allow high-throughput sample processing while decreasing the dependency on time-consuming culturing methods. The development of technologies for the detection and identification of pathogenic fungi and oomycetes is continuously evolving as new and innovative tools for sequencing and analyzing genomes become available. Advances in techniques such as qPCR, isothermal amplification, AmpliSeq technologies and portable tools that provide faster and easier detection capabilities will be presented in this Special Issue.
Dr. Guillaume Bilodeau
Manuscript Submission Information
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access monthly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.
- detection and identification of plant pests
- molecular detection
- molecular tools
- HTS detection
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Identification and Diferentiation of Pathogenic Fungi Genus Verticillium with PCR Markers and Sequencing of ITS Region
Taja Jeseničnik1, Anela Kaurin1, Jernej Jakše1, Sebastjan Radišek2, Branka Javornik1, Nataša Štajner1*
1 University of Ljubljana, Biotechnical Faculty, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
2 Slovenian Institute for Hop Research and Brewing, Plant Protection Department, Cesta Žalskega tabora 2, 3310 Žalec, Slovenia
* Corresponding author (email: [email protected])
Abstract: The genus Verticillium is a group of ascomycete fungi, including plant-pathogenic species capable of affecting vasculature of many agricultural crops and therefore causing big economic losses worldwide. In 2011 a new taxonomic classification of the genus was established which now referred to as Verticillium sensu stricto, comprises of ten species of plant-pathogenic fungi.
The main objective of the work is linked to the taxonomic classification and nomenclature of genus Verticillium sensu stricto as suggested by Inderbitzin et al. (2013). First, the isolates collected in Slovenian Institute of Hop Research and Brewing were analysed with simplex and multiplex PCR assays, designed by Inderbitzin et al (2013) to identify their origin in accordance to the new taxonomic classification. Second, the isolates’ ITS region was sequenced, and the resulted phylogeny analysis were compared to PCR analyses to determine the compatibility with the newly introduced PCR markers. Since the unambiguous identification using molecular markers is crucial for the analyses considering fungi, the third objective was to test whether some more routinely used marker system, e.g. highly polymorphic simple sequence repeats (SSR markers) are enough effective for accurate identification of isolates. In addition, we used set of 9 markers originating from lethal region of Verticillium nonalfalafe to show the variability of certain regions within Verticillium sensu stricto species.
With new PCR primers we were able to identify 88 isolates out of 105 isolates obtained from different geographic locations in Europe, North America and Japan and from different host plants including hop, potato, tomato, cotton, olive and alfalfa. Among all determined isolates, 6 were identified as V. albo-atrum, 5 as V. alfalfae, 28 as V. dahliae, 3 as V. isaacii, 1 as V. longisporum lineage A1/D1, 41 as V. nonalfalfae, 1 as V. nubilum and 2 as V. tricorpus. Identification and differentiation of V. longisporum linegaes was implemented by multiplex PCR assay.
Based on comparison of ITS sequencing and PCR/marker analysis reported previously we obtained some additional information about subgroups within species V. albo-atrum and V. dahliae.