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Microbial Population Genetics
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Microbial Population Genetics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (25 April 2023) | Viewed by 5672

Special Issue Editor

Prof. Dr. Jianping Xu

E-Mail Website
Guest Editor
Department of Biology, McMaster University, Ontario, Canada
Interests: microbiology; mycology; population genetics and genomics; infectious disease epidemiology; molecular ecology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Population genetics investigates the patterns of genetic variation within and between populations. It is a highly interdisciplinary field of study that uses knowledge of the rules of inheritance in genetic crosses to infer how the genetic composition of a population has changed in the past and to predict how such populations may change in the future under various forces of evolution. Population genetic studies provide the foundations upon which many other fields such as taxonomy, conservation management, crop breeding, and personalized medicine are based.

Microorganisms are among the most specious and diverse group of organisms. They are phylogenetically very diverse, are distributed across all ecological niches, and play major roles in each niche, from the bottom of oceans to the top of mountains, and from the equator to the Arctic and Antarctic. They both positively and negatively impact the health of plants, animals, and our ecosystems. While most microorganisms are not visible to the naked human eye most of the time, some microorganisms, such as mushrooms, form visible structures during at least part of their life cycles. Some of these mushrooms are considered delicacies in many cultures, while other mushroom-forming fungi may be extremely toxic to humans and other animals. Hundreds of viral, bacterial, and fungal species can directly cause human diseases, being responsible for a significant amount of morbidity and mortality each year. Furthermore, thousands of microbial species can cause infectious diseases in crop plants. Population genetic studies of these microbial pathogens have helped elucidate the epidemiology of infectious diseases, including the origin, transmission, and spread of novel genotypes and of virulent and drug-resistant strains. The recent revolution in molecular genetic tools, including genomics tools, is accelerating our understanding of microbial populations.

This Special Issue attempts to capture some of the recent exciting advancements in microbial population genetics. We welcome submissions on all groups of microbes, including viruses, bacteria, archaea, fungi, oomycetes, algae, protozoa, etc. Both original research papers and review papers are welcome. Our focus will be on studies using multiple molecular genetic markers, including whole-genome sequences, to analyze large number of strains of each species/species complex.

Prof. Dr. Jianping Xu
Guest Editor

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 submissions that pass pre-check are 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. Genes 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 2600 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

  • gene sequences
  • microsatellite markers
  • viruses
  • bacteria
  • archaea
  • fungi
  • landscape factors
  • mode of reproduction
  • cryptic speciation
  • selection
  • gene flow

Published Papers (3 papers)

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Research

14 pages, 3018 KiB  
Article
Differential Detection of Alternaria alternata Haplotypes Isolated from Carya illinoinensis Using PCR-RFLP Analysis of Alt a1 Gene Region
by Conrad Chibunna Achilonu, Marieka Gryzenhout, Gert Johannes Marais and Soumya Ghosh
Genes 2023, 14(5), 1115; https://doi.org/10.3390/genes14051115 - 20 May 2023
Cited by 3 | Viewed by 1533
Abstract
Alternaria black spot disease on pecan is caused by the opportunistic pathogen Alternaria alternata and poses a serious threat to the local South African and global pecan industry. Several diagnostic molecular marker applications have been established and used in the screening of various [...] Read more.
Alternaria black spot disease on pecan is caused by the opportunistic pathogen Alternaria alternata and poses a serious threat to the local South African and global pecan industry. Several diagnostic molecular marker applications have been established and used in the screening of various fungal diseases worldwide. The present study investigated the potential for polymorphism within samples of A. alternata isolates obtained from eight different geographical locations in South Africa. Pecan (Carya illinoinensis) leaves, shoots, and nuts-in-shuck with Alternaria black spot disease were sampled, and 222 A. alternata isolates were retrieved. For rapid screening to identify Alternaria black spot pathogens, polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of the Alternaria major allergen (Alt a1) gene region was used, followed by the digestion of the amplicons with HaeIII and HinfI endonucleases. The assay resulted in five (HaeIII) and two (HinfI) band patterns. Unique banding patterns from the two endonucleases showed the best profile and isolates were grouped into six clusters using a UPGMA (unweighted pair group method with arithmetic averages) distance matrix (Euclidean) dendrogram method on R-Studio. The analysis confirmed that the genetic diversity of A. alternata does not depend on host tissues or the pecan cultivation region. The grouping of selected isolates was confirmed by DNA sequence analysis. The Alt a1 phylogeny corroborated no speciation within the dendrogram groups and showed 98–100% bootstrap similarity. This study reports the first documented rapid and reliable technique for routine screening identification of pathogens causing Alternaria black spot in South Africa. Full article
(This article belongs to the Special Issue Microbial Population Genetics)
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15 pages, 2455 KiB  
Article
Phylogeographic Diversity Analysis of Bipolaris sorokiniana (Sacc.) Shoemaker Causing Spot Blotch Disease in Wheat and Barley
by Pradeep Sharma, Shefali Mishra, Garima Singroha, Rajan Selva Kumar, Sanjay Kumar Singh and Gyanendra Pratap Singh
Genes 2022, 13(12), 2206; https://doi.org/10.3390/genes13122206 - 24 Nov 2022
Cited by 4 | Viewed by 2013
Abstract
Bipolaris sorokiniana is a fungal pathogen that infects wheat, barley, and other crops, causing spot blotch disease. The disease is most common in humid, warm, wheat-growing regions, with South Asia’s Eastern Gangetic Plains serving as a hotspot. There is very little information known [...] Read more.
Bipolaris sorokiniana is a fungal pathogen that infects wheat, barley, and other crops, causing spot blotch disease. The disease is most common in humid, warm, wheat-growing regions, with South Asia’s Eastern Gangetic Plains serving as a hotspot. There is very little information known about its genetic variability, demography, and divergence period. The current work is the first to study the phylogeographic patterns of B. sorokiniana isolates obtained from various wheat and barley-growing regions throughout the world, with the goal of elucidating the demographic history and estimating divergence times. In this study, 162 ITS sequences, 18 GAPDH sequences, and 74 TEF-1α sequences from B. sorokiniana obtained from the GenBank, including 21 ITS sequences produced in this study, were used to analyse the phylogeographic pattern of distribution and evolution of B. sorokiniana infecting wheat and barley. The degrees of differentiation among B. sorokiniana sequences from eighteen countries imply the presence of a broad and geographically undifferentiated global population. The study provided forty haplotypes. The H_1 haplotype was identified to be the ancestral haplotype, followed by H_29 and H_27, with H_1 occupying a central position in the median-joining network and being shared by several populations from different continents. The phylogeographic patterns of species based on multi-gene analysis, as well as the predominance of a single haplotype, suggested that human-mediated dispersal may have played a significant role in shaping this pathogen’s population. According to divergence time analysis, haplogroups began at the Plio/Pleistocene boundary. Full article
(This article belongs to the Special Issue Microbial Population Genetics)
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17 pages, 750 KiB  
Article
Analyses of the Global Multilocus Genotypes of the Human Pathogenic Yeast Cryptococcus neoformans Species Complex
by Megan Hitchcock and Jianping Xu
Genes 2022, 13(11), 2045; https://doi.org/10.3390/genes13112045 - 6 Nov 2022
Cited by 7 | Viewed by 1590
Abstract
Cryptococcus neoformans species complex (CNSC) is a globally distributed human opportunistic yeast pathogen consisting of five major molecular types (VNI, VNII, VNB, VNIII and VNIV) belonging to two species, C. neoformans (VNI, VNII and VNB, collectively called serotype A) and C. deneoformans (VNIV, [...] Read more.
Cryptococcus neoformans species complex (CNSC) is a globally distributed human opportunistic yeast pathogen consisting of five major molecular types (VNI, VNII, VNB, VNIII and VNIV) belonging to two species, C. neoformans (VNI, VNII and VNB, collectively called serotype A) and C. deneoformans (VNIV, commonly called serotype D), and their hybrids (VNIII, serotype AD). Over the years, many studies have analyzed the geographical distribution and genetic diversity of CNSC. However, the global population structure and mode of reproduction remain incompletely described. In this study, we analyze the published multilocus sequence data at seven loci for CNSC. The combined sequences at the seven loci identified a total of 657 multilocus sequence types (STs), including 296 STs with known geographic information, representing 4200 non-redundant isolates from 31 countries and four continents. Among the 296 STs, 78 and 52 were shared among countries and continents, respectively, representing 3643 of the 4200 isolates. Except for the clone-corrected serotype D sample among countries, our analysis of the molecular variance of the 4200 isolates revealed significant genetic differentiations among countries and continents in populations of CNSC, serotype A, and serotype D. Phylogenetic analyses of the concatenated sequences of all 657 STs revealed several large clusters corresponding to the major molecular types. However, several rare but distinct STs were also found, representing potentially novel molecular types and/or hybrids of existing molecular types. Phylogenetic incompatibility analyses revealed evidence for recombination within all four major molecular types—VNI, VNII, VNIV and VNB—as well as within two VNB subclades, VNBI and VNBII, and two ST clusters around the most common STs, ST5 and ST93. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across most samples. Together, our results suggest evidence for historical differentiation, frequent recent gene flow, clonal expansion and recombination within and between lineages of the global CNSC population. Full article
(This article belongs to the Special Issue Microbial Population Genetics)
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