Applications of Genomics to Infectious Disease of Plants

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (30 June 2017) | Viewed by 11289

Special Issue Editor

Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
Interests: bioinformatics; genomics; xanthomonas; oomycetes

Special Issue Information

Dear Colleagues,

Microbial pathogens of plants have plagued farmers for millennia. Today, crop losses caused by fungal and oomycete pathogens would be enough to feed more than 8.5% of the world’s population; and that is not even counting losses due to bacteria and phytoplasmas. Recent technical developments in genomics methods offer new tools for fundamental research aimed at understanding the biology of these pathogens and their interactions with host plants. They have also enabled progress in tools for early detection and identification of pathogens, which is often essential for effective control of disease. Furthermore, innovations in sequencing ancient DNA have shed light on historical migration and spread of pathogens.

In this Special Issue, we invite investigators to submit manuscripts that cover this broad topic. These can include everything from novel uses of current sequencing technology to investigate phytopathogen genomics, to cutting edge applications of whole genome sequencing to “real world” scenarios. The topics are not just limited to genome sequencing, but also include applications of other large-scale “omics” technologies in plant pathology.

Dr. David J. Studholme
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 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.

Keywords

  • genomics
  • sequencing
  • pathogens
  • crops

Published Papers (2 papers)

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Research

1167 KiB  
Article
Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles
by Cassandra Collins, Rachel Hurley, Nada Almutlaqah, Grainne O’Keeffe, Thomas M. Keane, David A. Fitzpatrick and Rebecca A. Owens
Microorganisms 2017, 5(3), 60; https://doi.org/10.3390/microorganisms5030060 - 17 Sep 2017
Cited by 11 | Viewed by 5694
Abstract
Armillaria mellea is a major plant pathogen. Yet, the strategies the organism uses to infect susceptible species, degrade lignocellulose and other plant material and protect itself against plant defences and its own glycodegradative arsenal are largely unknown. Here, we use a combination of [...] Read more.
Armillaria mellea is a major plant pathogen. Yet, the strategies the organism uses to infect susceptible species, degrade lignocellulose and other plant material and protect itself against plant defences and its own glycodegradative arsenal are largely unknown. Here, we use a combination of gel and MS-based proteomics to profile A. mellea under conditions of oxidative stress and changes in growth matrix. 2-DE and LC-MS/MS were used to investigate the response of A. mellea to H2O2 and menadione/FeCl3 exposure, respectively. Several proteins were detected with altered abundance in response to H2O2, but not menadione/FeCl3 (i.e., valosin-containing protein), indicating distinct responses to these different forms of oxidative stress. One protein, cobalamin-independent methionine synthase, demonstrated a common response in both conditions, which may be a marker for a more general stress response mechanism. Further changes to the A. mellea proteome were investigated using MS-based proteomics, which identified changes to putative secondary metabolism (SM) enzymes upon growth in agar compared to liquid cultures. Metabolomic analyses revealed distinct profiles, highlighting the effect of growth matrix on SM production. This establishes robust methods by which to utilize comparative proteomics to characterize this important phytopathogen. Full article
(This article belongs to the Special Issue Applications of Genomics to Infectious Disease of Plants)
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693 KiB  
Article
Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae
by Ryan M. Ames
Microorganisms 2017, 5(1), 3; https://doi.org/10.3390/microorganisms5010003 - 17 Jan 2017
Cited by 6 | Viewed by 5334
Abstract
Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world’s population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages [...] Read more.
Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world’s population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified. In this study, I have used network-extracted ontologies (NeXOs), hierarchical structures inferred from RNA-Seq data, to identify pathways involved in appressorium development, which in turn highlights novel genes with potential roles in this process. This study illustrates the use of NeXOs for pathway identification from large-scale genomics data and also identifies novel genes with potential roles in disease. The methods presented here will be useful to study disease processes in other pathogenic species and these data represent predictions of novel targets for intervention in M. oryzae. Full article
(This article belongs to the Special Issue Applications of Genomics to Infectious Disease of Plants)
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