Special Issue "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: 25 April 2023 | Viewed by 935

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

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Keywords

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

Published Papers (2 papers)

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Research

Article
Phylogeographic Diversity Analysis of Bipolaris sorokiniana (Sacc.) Shoemaker Causing Spot Blotch Disease in Wheat and Barley
Genes 2022, 13(12), 2206; https://doi.org/10.3390/genes13122206 - 24 Nov 2022
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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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Article
Analyses of the Global Multilocus Genotypes of the Human Pathogenic Yeast Cryptococcus neoformans Species Complex
Genes 2022, 13(11), 2045; https://doi.org/10.3390/genes13112045 - 06 Nov 2022
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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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