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Special Issue "Genomics: Infectious Disease and Host-Pathogen Interaction"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 31 December 2021.

Special Issue Editors

Prof. Dr. Akira Ishihama
E-Mail Website
Guest Editor
Department of Frontier Bioscience, Hosei University, Tokyo 184-8584, Japan
Interests: bacteriology; escherichia coli; bacterial genome regulation
Dr. Franklin W.N. Chow
E-Mail Website
Guest Editor
Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
Interests: infectious diseases; host–pathogen interactions; extracellular vesicles; pathogen genomics and evolution; RNA biology
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

Infectious diseases are disorders caused by pathogens, such as bacteria, viruses, fungi or parasites, and pose a serious threat to humans, animals, and plants. Pathogens can interact with the host to suppress or evade the host immune system in order to establish and disseminate infections.

Unique genome features contribute largely to the events of host–pathogen interactions, governing the virulence level of the pathogens and the infection severity of the host. With the advancement of NGS and nanopore sequencings, it is now highly cost-effective to pursue genomic and transcriptomic studies. Recent research has shown that host–pathogen interactions can be bi-directionally modulated by small RNAs that come from unique genome loci. Under the current COVID-19 pandemic, there has been a surge in development of SARS-CoV-2 detection methods based on studying the phylogenomics and mutations of viral genomes.

We invite researchers to contribute original research articles and reviews focused on different genomic aspects of 1) infectious diseases, and ii) host–pathogen interactions.

Topics of interest include, but are not limited to, the following:

- Genomics and transcriptomics;

- Phylogenetics and evolution;

- Small RNA regulations;

- RNA biology (e.g., dual-RNA-seq);

- Molecular pathogenesis;

- Molecular detection.

Prof. Dr. Akira Ishihama
Dr. Franklin W.N. Chow
Guest Editors

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • Infectious diseases
  • NGS
  • Small RNA
  • Host–pathogen interaction
  • Pathogen detection
  • Viruses
  • Fungi
  • Parasites
  • Bacteria
  • Evolution

Published Papers (2 papers)

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Research

Article
alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein–Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria
Int. J. Mol. Sci. 2021, 22(15), 8342; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22158342 - 03 Aug 2021
Viewed by 580
Abstract
Alfalfa has emerged as one of the most important forage crops, owing to its wide adaptation and high biomass production worldwide. In the last decade, the emergence of bacterial stem blight (caused by Pseudomonas syringae pv. syringae ALF3) in alfalfa has caused around [...] Read more.
Alfalfa has emerged as one of the most important forage crops, owing to its wide adaptation and high biomass production worldwide. In the last decade, the emergence of bacterial stem blight (caused by Pseudomonas syringae pv. syringae ALF3) in alfalfa has caused around 50% yield losses in the United States. Studies are being conducted to decipher the roles of the key genes and pathways regulating the disease, but due to the sparse knowledge about the infection mechanisms of Pseudomonas, the development of resistant cultivars is hampered. The database alfaNET is an attempt to assist researchers by providing comprehensive Pseudomonas proteome annotations, as well as a host–pathogen interactome tool, which predicts the interactions between host and pathogen based on orthology. alfaNET is a user-friendly and efficient tool and includes other features such as subcellular localization annotations of pathogen proteins, gene ontology (GO) annotations, network visualization, and effector protein prediction. Users can also browse and search the database using particular keywords or proteins with a specific length. Additionally, the BLAST search tool enables the user to perform a homology sequence search against the alfalfa and Pseudomonas proteomes. With the successful implementation of these attributes, alfaNET will be a beneficial resource to the research community engaged in implementing molecular strategies to mitigate the disease. alfaNET is freely available for public use at http://bioinfo.usu.edu/alfanet/. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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Article
Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits
Int. J. Mol. Sci. 2021, 22(12), 6202; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22126202 - 08 Jun 2021
Viewed by 710
Abstract
Red pepper (Capsicum annuum, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three [...] Read more.
Red pepper (Capsicum annuum, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three different fields. We compared two different library types and three different analytical methods for the identification of microbiomes in overwintering pepper fruits. Our results demonstrated that DNA sequencing might be useful for the identification of bacteria and DNA viruses such as bacteriophages, while mRNA sequencing might be beneficial for the identification of fungi and RNA viruses. Among three analytical methods, KRAKEN2 with raw data reads (KRAKEN2_R) might be superior for the identification of microbial species to other analytical methods. However, some microbial species with a low number of reads were wrongly assigned at the species level by KRAKEN2_R. Moreover, we found that the databases for bacteria and viruses were better established as compared to the fungal database with limited genome data. In summary, we carefully suggest that different library types and analytical methods with proper databases should be applied for the purpose of microbiome study. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction)
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