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Whole-Genome Sequencing and Population Genomics of Parasitic Infections
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Whole-Genome Sequencing and Population Genomics of Parasitic Infections

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

Deadline for manuscript submissions: closed (25 November 2020) | Viewed by 27585

Special Issue Editor

Dr. Asis Khan

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Guest Editor
Laboratory of Parasitic Diseases, National Institue of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20892, USA
Interests: whole genome sequencing; population genetics; comparative genomomics; parasitic infections

Special Issue Information

Dear Colleagues,

Parasitic diseases contribute substantially to the global burden of disease, infecting hundreds of millions of people around the world. Alone, the malaria-causing agent Plasmodium infects more than 210 million people around the globe and kills 660,000 people each year, mostly young children in sub-Saharan Africa. Additionally, Neglected Tropical Diseases (NTDs), which include Chagas disease, onchocerciasis, schistosomiasis, guinea-worm disease, sleeping sickness, leishmaniases, and lymphatic filariasis affect more than one-sixth of the world’s population and account for approximately 26 million disability-adjusted life years (DALYs). In the absence of vaccines, the prevention of these parasitic diseases relies solely on chemotherapy, which is far from perfect and is constantly challenged by parasites evolving drug resistance. Thus, there is an urgent need to broaden therapeutic horizons against these parasitic infections, and to do so, we need to have comprehensive knowledge of their life cycles, their genomes, and their population genetic structures. This understanding is critical to evaluating the impact of transmission methods in fixing and spreading important genes related to virulence and drug resistance through populations. With the advent of next-generation sequencing (NGS), comparative genomics has revolutionized our understanding of the architecture of parasitic genomes and how they are evolving and establishing within the population, including the role of asexual versus sexual recombination in this process. Hence, the overarching theme of this Special Issue is the recent advances in NGS, comparative genomics, and evolution analysis that have accelerated the field’s progress in understanding population genomics and in developing new therapeutics against these parasitic diseases.

Dr. Asis Khan
Guest Editor

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Keywords

  • parasitic diseases
  • neglected tropical diseases
  • sexual and asexual transmission
  • whole genome sequencing
  • comparative genomics
  • population genetic structure
  • recombination
  • homozygosity and heterozygosity
  • selfing
  • outcrossing
  • mapping
  • variants

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Published Papers (6 papers)

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Research

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16 pages, 3622 KiB  
Article
Leishmania Sexual Reproductive Strategies as Resolved through Computational Methods Designed for Aneuploid Genomes
by Jahangheer S. Shaik, Deborah E. Dobson, David L. Sacks and Stephen M. Beverley
Genes 2021, 12(2), 167; https://doi.org/10.3390/genes12020167 - 26 Jan 2021
Cited by 15 | Viewed by 3149
Abstract
A cryptic sexual reproductive cycle in Leishmania has been inferred through population genetic studies revealing the presence of hybrid genotypes in natural isolates, with attempts made to decipher sexual strategies by studying complex chromosomal inheritance patterns. A more informative approach is to study [...] Read more.
A cryptic sexual reproductive cycle in Leishmania has been inferred through population genetic studies revealing the presence of hybrid genotypes in natural isolates, with attempts made to decipher sexual strategies by studying complex chromosomal inheritance patterns. A more informative approach is to study the products of controlled, laboratory-based experiments where known strains or species are crossed in the sand fly vector to generate hybrid progeny. These hybrids can be subsequently studied through high resolution sequencing technologies and software suites such as PAINT that disclose inheritance patterns including ploidies, parental chromosome contributions and recombinations, all of which can inform the sexual strategy. In this work, we discuss the computational methods in PAINT that can be used to interpret the sexual strategies adopted specifically by aneuploid organisms and summarize how PAINT has been applied to the analysis of experimental hybrids to reveal meiosis-like sexual recombination in Leishmania. Full article
(This article belongs to the Special Issue Whole-Genome Sequencing and Population Genomics of Parasitic Infections)
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17 pages, 1829 KiB  
Article
Parasite Presence Induces Gene Expression Changes in an Ant Host Related to Immunity and Longevity
by Marah Stoldt, Linda Klein, Sara Beros, Falk Butter, Evelien Jongepier, Barbara Feldmeyer and Susanne Foitzik
Genes 2021, 12(1), 95; https://doi.org/10.3390/genes12010095 - 13 Jan 2021
Cited by 10 | Viewed by 6291
Abstract
Most species are either parasites or exploited by parasites, making parasite–host interactions a driver of evolution. Parasites with complex life cycles often evolve strategies to facilitate transmission to the definitive host by manipulating their intermediate host. Such manipulations could explain phenotypic changes in [...] Read more.
Most species are either parasites or exploited by parasites, making parasite–host interactions a driver of evolution. Parasites with complex life cycles often evolve strategies to facilitate transmission to the definitive host by manipulating their intermediate host. Such manipulations could explain phenotypic changes in the ant Temnothorax nylanderi, the intermediate host of the cestode Anomotaenia brevis. In addition to behavioral and morphological alterations, infected workers exhibit prolonged lifespans, comparable to that of queens, which live up to two decades. We used transcriptomic data from cestodes and ants of different castes and infection status to investigate the molecular underpinnings of phenotypic alterations in infected workers and explored whether the extended lifespan of queens and infected workers has a common molecular basis. Infected workers and queens commonly upregulated only six genes, one of them with a known anti-aging function. Both groups overexpressed immune genes, although not the same ones. Our findings suggest that the lifespan extension of infected workers is not achieved via the expression of queen-specific genes. The analysis of the cestodes’ transcriptome revealed dominant expression of genes of the mitochondrial respiratory transport chain, which indicates an active metabolism and shedding light on the physiology of the parasite in its cysticercoid stage. Full article
(This article belongs to the Special Issue Whole-Genome Sequencing and Population Genomics of Parasitic Infections)
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Review

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12 pages, 448 KiB  
Review
Challenges for Cryptosporidium Population Studies
by Rodrigo P. Baptista, Garrett W. Cooper and Jessica C. Kissinger
Genes 2021, 12(6), 894; https://doi.org/10.3390/genes12060894 - 10 Jun 2021
Cited by 12 | Viewed by 4124
Abstract
Cryptosporidiosis is ranked sixth in the list of the most important food-borne parasites globally, and it is an important contributor to mortality in infants and the immunosuppressed. Recently, the number of genome sequences available for this parasite has increased drastically. The majority of [...] Read more.
Cryptosporidiosis is ranked sixth in the list of the most important food-borne parasites globally, and it is an important contributor to mortality in infants and the immunosuppressed. Recently, the number of genome sequences available for this parasite has increased drastically. The majority of the sequences are derived from population studies of Cryptosporidium parvum and Cryptosporidium hominis, the most important species causing disease in humans. Work with this parasite is challenging since it lacks an optimal, prolonged, in vitro culture system, which accurately reproduces the in vivo life cycle. This obstacle makes the cloning of isolates nearly impossible. Thus, patient isolates that are sequenced represent a population or, at times, mixed infections. Oocysts, the lifecycle stage currently used for sequencing, must be considered a population even if the sequence is derived from single-cell sequencing of a single oocyst because each oocyst contains four haploid meiotic progeny (sporozoites). Additionally, the community does not yet have a set of universal markers for strain typing that are distributed across all chromosomes. These variables pose challenges for population studies and require careful analyses to avoid biased interpretation. This review presents an overview of existing population studies, challenges, and potential solutions to facilitate future population analyses. Full article
(This article belongs to the Special Issue Whole-Genome Sequencing and Population Genomics of Parasitic Infections)
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18 pages, 1381 KiB  
Review
Malaria in the ‘Omics Era’
by Mirko Pegoraro and Gareth D. Weedall
Genes 2021, 12(6), 843; https://doi.org/10.3390/genes12060843 - 30 May 2021
Cited by 4 | Viewed by 3397
Abstract
Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome [...] Read more.
Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth—the number of Plasmodium species’ genomes sequenced—and in depth—massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology. Full article
(This article belongs to the Special Issue Whole-Genome Sequencing and Population Genomics of Parasitic Infections)
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15 pages, 543 KiB  
Review
Genomics of the Parasitic Nematode Ascaris and Its Relatives
by Jianbin Wang
Genes 2021, 12(4), 493; https://doi.org/10.3390/genes12040493 - 28 Mar 2021
Cited by 16 | Viewed by 5201
Abstract
Nematodes of the genus Ascaris are important parasites of humans and swine, and the phylogenetically related genera (Parascaris, Toxocara, and Baylisascaris) infect mammals of veterinary interest. Over the last decade, considerable genomic resources have been established for Ascaris, including complete [...] Read more.
Nematodes of the genus Ascaris are important parasites of humans and swine, and the phylogenetically related genera (Parascaris, Toxocara, and Baylisascaris) infect mammals of veterinary interest. Over the last decade, considerable genomic resources have been established for Ascaris, including complete germline and somatic genomes, comprehensive mRNA and small RNA transcriptomes, as well as genome-wide histone and chromatin data. These datasets provide a major resource for studies on the basic biology of these parasites and the host–parasite relationship. Ascaris and its relatives undergo programmed DNA elimination, a highly regulated process where chromosomes are fragmented and portions of the genome are lost in embryonic cells destined to adopt a somatic fate, whereas the genome remains intact in germ cells. Unlike many model organisms, Ascaris transcription drives early development beginning prior to pronuclear fusion. Studies on Ascaris demonstrated a complex small RNA network even in the absence of a piRNA pathway. Comparative genomics of these ascarids has provided perspectives on nematode sex chromosome evolution, programmed DNA elimination, and host–parasite coevolution. The genomic resources enable comparison of proteins across diverse species, revealing many new potential drug targets that could be used to control these parasitic nematodes. Full article
(This article belongs to the Special Issue Whole-Genome Sequencing and Population Genomics of Parasitic Infections)
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14 pages, 870 KiB  
Review
Exploring Eimeria Genomes to Understand Population Biology: Recent Progress and Future Opportunities
by Damer P. Blake, Kate Worthing and Mark C. Jenkins
Genes 2020, 11(9), 1103; https://doi.org/10.3390/genes11091103 - 21 Sep 2020
Cited by 24 | Viewed by 4458
Abstract
Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, [...] Read more.
Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control. Full article
(This article belongs to the Special Issue Whole-Genome Sequencing and Population Genomics of Parasitic Infections)
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