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Genetics of Leishmania
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Genetics of Leishmania

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

Deadline for manuscript submissions: closed (30 August 2019) | Viewed by 16934

Special Issue Editor

Dr. Gabriele Schönian

E-Mail Website
Guest Editor
Institute of Microbiology and Hygiene, University of Medicine Berlin, 10117 Berlin, Germany
Interests: taxonomy, phylogeny and population genetics of Leishmania genus; detection of inter- and intraspecific variation between leishmanial parasites
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues

Genes is announcing a Special Issue on “Genetics of Leishmania” for 2019, which will be open for studies on different aspects of genomics, genetics, and gene research in Leishmania parasites.

Reference genomes have been published for many Leishmania species and are available on the kinetoplastid genome database, TriTrypDB, together with unpublished assemblies for other species and strains. Although consistent, high-quality automated annotation is now possible, manual inspection and improvement of annotation is still critical. Genome-wide approaches have, so far, proved their potential for improving Leishmania taxonomy and exploring the origin of the genus, and for studying the microevolution of leishmanial populations. A comparison of different leishmanial genomes revealed a remarkable conservation of gene content and synteny in orthologous chromosomes and confirmed the significance of variable aneuploidy in these parasites, which seems to be adaptive and to depend on their life stage. Exploring the extent of genomic diversity in species and strains of Leishmania in comparison with phenotypic variations will help one to better understand the interplay between parasites, vectors, and hosts, and for developing effective drug and immunotherapeutic interventions.

We invite publications from scientists using genomic or genetic smaller-scale genetic approaches, including bioinformatics, to detect variations in coding or non-coding regions of leishmanial genomes. We are also interested in studies investigating the relations between genotypic and phenotypic diversity. Finally, we encourage the publication of population genetic, phylogenomic, and phylogenetic studies for Leishmania.

Dr. Gabriele Schönian
Guest Editor

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Keywords

  • Leishmania genus
  • Whole-genome sequencing
  • Genomic diversity
  • Bioinformatic tools
  • Genetic variation
  • Inter- and intraspecific variations
  • Population genetic studies
  • Phylogeny and phylogenomics
  • Taxonomy
  • Virulence determinants
  • Drug resistance
  • Immunogenic determinants
  • Molecular epidemiology
  • Parasite–host interplay

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Published Papers (4 papers)

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Research

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15 pages, 1664 KiB  
Article
Environmental Conditions May Shape the Patterns of Genomic Variations in Leishmania panamensis
by Carlos M. Restrepo, Alejandro Llanes, Eymi M. Cedeño, Jim H. Chang, Jennifer Álvarez, Margarita Ríos, Homero Penagos, José A. Suárez and Ricardo Lleonart
Genes 2019, 10(11), 838; https://doi.org/10.3390/genes10110838 - 24 Oct 2019
Cited by 8 | Viewed by 2814
Abstract
Due to the absence of transcriptional regulation of gene expression in Leishmania parasites, it is now well accepted that several forms of genomic variations modulate the levels of critical proteins through changes in gene dosage. We previously observed many of these variations in [...] Read more.
Due to the absence of transcriptional regulation of gene expression in Leishmania parasites, it is now well accepted that several forms of genomic variations modulate the levels of critical proteins through changes in gene dosage. We previously observed many of these variations in our reference laboratory strain of L. panamensis (PSC-1 strain), including chromosomes with an increased somy and the presence of a putative linear minichromosome derived from chromosome 34. Here, we compared the previously described genomic variations with those occurring after exposure of this strain to increasing concentrations of trivalent antimony (SbIII), as well as those present in two geographically unrelated clinical isolates of L. panamensis. We observed changes in the somy of several chromosomes, amplifications of several chromosomal regions, and copy number variations in gene arrays after exposure to SbIII. Occurrence of amplifications potentially beneficial for the Sb-resistant phenotype appears to be associated with the loss of other forms of amplification, such as the linear minichromosome. In contrast, we found no evidence of changes in somy or amplification of relatively large chromosomal regions in the clinical isolates. In these isolates, the predominant amplifications appear to be those that generate genes arrays; however, in many cases, the amplified arrays have a notably higher number of copies than those from the untreated and Sb-treated laboratory samples. Full article
(This article belongs to the Special Issue Genetics of Leishmania)
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10 pages, 1145 KiB  
Article
Molecular Characterization of Leishmania RNA virus 2 in Leishmania major from Uzbekistan
by Yuliya Kleschenko, Danyil Grybchuk, Nadezhda S. Matveeva, Diego H. Macedo, Evgeny N. Ponirovsky, Alexander N. Lukashev and Vyacheslav Yurchenko
Genes 2019, 10(10), 830; https://doi.org/10.3390/genes10100830 - 21 Oct 2019
Cited by 23 | Viewed by 4039
Abstract
Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan [...] Read more.
Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan and the viral sequences differed by only nineteen SNPs, all except one being silent mutations. Therefore, we concluded that they belong to a single LRV2 species. New viruses are closely related to the LRV2-Lmj-ASKH documented in Turkmenistan in 1995, which is congruent with their shared host (L. major) and common geographical origin. Full article
(This article belongs to the Special Issue Genetics of Leishmania)
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19 pages, 2919 KiB  
Article
Leishmania Mitochondrial Genomes: Maxicircle Structure and Heterogeneity of Minicircles
by Esther Camacho, Alberto Rastrojo, África Sanchiz, Sandra González-de la Fuente, Begoña Aguado and Jose M. Requena
Genes 2019, 10(10), 758; https://doi.org/10.3390/genes10100758 - 26 Sep 2019
Cited by 24 | Viewed by 5567
Abstract
The mitochondrial DNA (mtDNA), which is present in almost all eukaryotic organisms, is a useful marker for phylogenetic studies due to its relative high conservation and its inheritance manner. In Leishmania and other trypanosomatids, the mtDNA (also referred to as kinetoplast DNA or [...] Read more.
The mitochondrial DNA (mtDNA), which is present in almost all eukaryotic organisms, is a useful marker for phylogenetic studies due to its relative high conservation and its inheritance manner. In Leishmania and other trypanosomatids, the mtDNA (also referred to as kinetoplast DNA or kDNA) is composed of thousands of minicircles and a few maxicircles, catenated together into a complex network. Maxicircles are functionally similar to other eukaryotic mtDNAs, whereas minicircles are involved in RNA editing of some maxicircle-encoded transcripts. Next-generation sequencing (NGS) is increasingly used for assembling nuclear genomes and, currently, a large number of genomic sequences are available. However, most of the time, the mitochondrial genome is ignored in the genome assembly processes. The aim of this study was to develop a pipeline to assemble Leishmania minicircles and maxicircle DNA molecules, exploiting the raw data generated in the NGS projects. As a result, the maxicircle molecules and the plethora of minicircle classes for Leishmania major, Leishmania infantum and Leishmania braziliensis have been characterized. We have observed that whereas the heterogeneity of minicircle sequences existing in a single cell hampers their use for Leishmania typing and classification, maxicircles emerge as an extremely robust genetic marker for taxonomic studies within the clade of kinetoplastids. Full article
(This article belongs to the Special Issue Genetics of Leishmania)
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Review

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11 pages, 860 KiB  
Review
Trans-Atlantic Spillover: Deconstructing the Ecological Adaptation of Leishmania infantum in the Americas
by Mariana C. Boité, Gerald F. Späth, Giovanni Bussotti, Renato Porrozzi, Fernanda N. Morgado, Martin Llewellyn, Philipp Schwabl and Elisa Cupolillo
Genes 2020, 11(1), 4; https://doi.org/10.3390/genes11010004 - 19 Dec 2019
Cited by 10 | Viewed by 4040
Abstract
Pathogen fitness landscapes change when transmission cycles establish in non-native environments or spill over into new vectors and hosts. The introduction of Leishmania infantum in the Americas into the Neotropics during European colonization represents a unique case study to investigate the mechanisms of [...] Read more.
Pathogen fitness landscapes change when transmission cycles establish in non-native environments or spill over into new vectors and hosts. The introduction of Leishmania infantum in the Americas into the Neotropics during European colonization represents a unique case study to investigate the mechanisms of ecological adaptation of this important parasite. Defining the evolutionary trajectories that drive L. infantum fitness in this new environment are of great public health importance as they will allow unique insight into pathways of host/pathogen co-evolution and their consequences for region-specific changes in disease manifestation. This review summarizes current knowledge on L. infantum genetic and phenotypic diversity in the Americas and its possible role in the unique epidemiology of visceral leishmaniasis (VL) in the New World. We highlight the importance of appreciating adaptive molecular mechanisms in L. infantum to understand the parasite’s successful establishment on the continent. Full article
(This article belongs to the Special Issue Genetics of Leishmania)
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