Phylogenetic Studies

Kuhls, Katrin; Maurício, Isabel

doi:10.1007/978-1-4939-9210-2_2

Cited by 5 publications

(6 citation statements)

References 124 publications

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“…Moreover, the fact that most maxicircle-encoded transcripts require specific addition and deletion of uridine residues by the RNA editing machinery to form translatable mRNAs introduces an additional evolutionary variability among the orthologous genes. Notably, a maxicircle gene, cytochrome b (Cyb; Figure 1 ), is a classic and widely used marker for phylogenetic studies [ 50 , 51 ], but it is known that cytochrome b sequences cannot discriminate species such as L. donovani and L. infantum , or L. braziliensis and L. peruviana [ 10 ].…”

Section: Resultsmentioning

confidence: 99%

Assembly of a Large Collection of Maxicircle Sequences and Their Usefulness for Leishmania Taxonomy and Strain Typing

Solana

Chicharro

García

et al. 2022

Genes

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Parasites of medical importance, such as Leishmania and Trypanosoma, are characterized by the presence of thousands of circular DNA molecules forming a structure known as kinetoplast, within the mitochondria. The maxicircles, which are equivalent to the mitochondrial genome in other eukaryotes, have been proposed as a promising phylogenetic marker. Using whole-DNA sequencing data, it is also possible to assemble maxicircle sequences as shown here and in previous works. In this study, based on data available in public databases and using a bioinformatics workflow previously reported by our group, we assembled the complete coding region of the maxicircles for 26 prototypical strains of trypanosomatid species. Phylogenetic analysis based on this dataset resulted in a robust tree showing an accurate taxonomy of kinetoplastids, which was also able to discern between closely related Leishmania species that are usually difficult to discriminate by classical methodologies. In addition, we provide a dataset of the maxicircle sequences of 60 Leishmania infantum field isolates from America, Western Europe, North Africa, and Eastern Europe. In agreement with previous studies, our data indicate that L. infantum parasites from Brazil are highly homogeneous and closely related to European strains, which were transferred there during the discovery of America. However, this study showed the existence of different L. infantum populations/clades within the Mediterranean region. A maxicircle signature for each clade has been established. Interestingly, two L. infantum clades were found coexisting in the same region of Spain, one similar to the American strains, represented by the Spanish JPCM5 reference strain, and the other, named “non-JPC like”, may be related to an important leishmaniasis outbreak that occurred in Madrid a few years ago. In conclusion, the maxicircle sequence emerges as a robust molecular marker for phylogenetic analysis and species typing within the kinetoplastids, which also has the potential to discriminate intraspecific variability.

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Section: Resultsmentioning

confidence: 99%

Assembly of a Large Collection of Maxicircle Sequences and Their Usefulness for Leishmania Taxonomy and Strain Typing

Solana

Chicharro

García

et al. 2022

Genes

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“…In fact, the sequence of the cytochrome b (Cyt b) gene, which is part of the maxicircle, is being used in many studies for phylogeny analysis within the Leishmania genus [63,64]. Moreover, the Cyt b gene is included in many of the multilocus sequence typing (MLST) sets currently used for phylogenetic studies in Leishmania [65]. MLST is based on the use of concatenated sequences from several genes and is aimed to ensure robust phylogenetic inferences.…”

Section: Discussionmentioning

confidence: 99%

Leishmania Mitochondrial Genomes: Maxicircle Structure and Heterogeneity of Minicircles

Camacho

Rastrojo

Sanchiz

et al. 2019

Genes

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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.

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“…Many markers and techniques have been used for Leishmania identification, as reviewed (Akhoundi et al., 2017; Kuhls & Mauricio, 2019; Van der Auwera & Dujardin, 2015). Nevertheless, in most studies, they have been applied to a low number of strains, to strains isolated only from the Old or New World, without covering both Leishmania and Viannia subgenera, or are limited to a single technique.…”

Section: Discussionmentioning

confidence: 99%

“…A third approach is sequencing, which generally takes up an intermediate position regarding discriminative power, workability and time consumption, but its pros and cons are hardly influenced by the target used (Kuhls & Mauricio, 2019). In the current study, the four analysed genetic regions permitted a confident identification of the Leishmania subgenus at the species level.…”

Section: Discussionmentioning

confidence: 99%

“…Nevertheless, the amplicon length could preliminarily orientate towards certain complexes. Finally, even if not applied here, another factor worth considering is that some of the used regions work well with small amounts of DNA, being directly available from a clinical sample (Kuhls & Mauricio, 2019; Montalvo et al., 2017; Schönian et al., 2003); a trait inapplicable for MLEE or MALDI‐TOF. This reduces costs and other culture difficulties, but drawbacks could arise related to the sensitivity of the technique.…”

Section: Discussionmentioning

confidence: 99%

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Autochthonous and imported tegumentary leishmaniasis in Catalonia (Spain): Aetiological evolution in the last four decades and usefulness of different typing approaches based on biochemical, molecular and proteomic markers

Fernández-Arévalo

Ballart

Muñoz-Basagoiti

et al. 2021

Transbounding Emerging Dis

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Leishmaniasis is a transmissible disease caused by Leishmania protozoa. Spain is endemic for both visceral and cutaneous leishmaniasis, the autochthonous aetiological agent being Leishmania infantum. Around the world, the L. donovani complex is associated with visceral symptoms, while any species of the Leishmania or Viannia subgenera affecting human can produce tegumentary forms. In a context of growing numbers of imported cases, associated with globalisation, the aim of this study was to analyse the aetiological evolution of human tegumentary leishmaniasis in a region of Spain (Catalonia). Fifty‐six Leishmania strains, isolated from 1981 to 2018, were analysed using MLEE, gene sequencing (hsp70, rpoIILS, fh and ITS2) and MALDI‐TOF. The utility of these different analytical methods was compared. The results showed an increase in leishmaniasis over the two last decades, particularly imported cases, which represented 39% of all cases studied. Leishmania infantum, L. major, L. tropica, L. braziliensis, L. guyanensis and L. panamensis were identified. The combination of molecular and enzymatic methods allowed the identification of 29 different strain types (A to AC). Strain diversity was higher in L. (Viannia), whilst the different L. major types were relatable with geo‐temporal data. Among the autochthonous cases, type C prevailed throughout the studied period (39%). Minor types generally appeared within a short time interval. While all the techniques provided identical identification at the species complex level, MALDI‐TOF and rpoIILS or fh sequencing would be the most suitable identification tools for clinical practice, and the tandem hsp70‐ITS2 could substitute MLEE in the epidemiological field.

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Phylogenetic Studies

Cited by 5 publications

References 124 publications

Assembly of a Large Collection of Maxicircle Sequences and Their Usefulness for Leishmania Taxonomy and Strain Typing

Assembly of a Large Collection of Maxicircle Sequences and Their Usefulness for Leishmania Taxonomy and Strain Typing

Leishmania Mitochondrial Genomes: Maxicircle Structure and Heterogeneity of Minicircles

Autochthonous and imported tegumentary leishmaniasis in Catalonia (Spain): Aetiological evolution in the last four decades and usefulness of different typing approaches based on biochemical, molecular and proteomic markers

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