1
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Gerasimov ES, Novozhilova TS, Zimmer SL, Yurchenko V. Kinetoplast Genome of Leishmania spp. Is under Strong Purifying Selection. Trop Med Infect Dis 2023; 8:384. [PMID: 37624322 PMCID: PMC10458658 DOI: 10.3390/tropicalmed8080384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Instability is an intriguing characteristic of many protist genomes, and trypanosomatids are not an exception in this respect. Some regions of trypanosomatid genomes evolve fast. For instance, the trypanosomatid mitochondrial (kinetoplast) genome consists of fairly conserved maxicircle and minicircle molecules that can, nevertheless, possess high nucleotide substitution rates between closely related strains. Recent experiments have demonstrated that rapid laboratory evolution can result in the non-functionality of multiple genes of kinetoplast genomes due to the accumulation of mutations or loss of critical genomic components. An example of a loss of critical components is the reported loss of entire minicircle classes in Leishmania tarentolae during laboratory cultivation, which results in an inability to generate some correctly encoded genes. In the current work, we estimated the evolutionary rates of mitochondrial and nuclear genome regions of multiple natural Leishmania spp. We analyzed synonymous and non-synonymous substitutions and, rather unexpectedly, found that the coding regions of kinetoplast maxicircles are among the most variable regions of both genomes. In addition, we demonstrate that synonymous substitutions greatly predominate among maxicircle coding regions and that most maxicircle genes show signs of purifying selection. These results imply that maxicircles in natural Leishmania populations remain functional despite their high mutation rate.
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Affiliation(s)
- Evgeny S. Gerasimov
- Department of Molecular Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia
| | - Tatiana S. Novozhilova
- Department of Molecular Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Sara L. Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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2
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Spotin A, Rouhani S, Haghighi A, Parvizi P. Low genetic heterogeneity of Leishmania major in different geographical regions of Iran. PLoS One 2023; 18:e0285520. [PMID: 37155684 PMCID: PMC10166485 DOI: 10.1371/journal.pone.0285520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
To examine the genetic diversity of Leishmania major, 100 Giemsa-stained positive slides were collected from endemic foci of Iran (Northeast, Central, and Southwest provinces) over two consecutive years during 2019-2021. The Leishmania ITS-rDNA gene was amplified and Leishmania sp. was recognized by PCR-RFLP and sequencing. In addition, 178 registered ITS-rDNA sequences from other geographical regions of Iran were retrieved from GenBank, including different host species (human, sandfly and rodent). A total of 40 new haplotypes were discovered using the ITS-rDNA sequence analysis. IR29 (20.6%) and IR34 (61%) were the two most common haplotypes, represented by a star-like feature in the overall population. Analysis of the molecular variance test revealed low genetic diversity of L. major in human cases (Haplotype diversity; 0.341), rodent (Hd; 0.387) and sandfly (Hd; 0.390) sequences. The lowest genetic diversity of L. major was observed in Southwest/Southeast Iran (Hd: 0.104-0.286). The statistically Fst value indicated that L. major is not genetically differentiated between geographic regions of Iran, except for the Northeast-Southwest (Fst: 0.29055) and Central-Southwest (Fst: 0.30294) population pairs. The current study as the first investigation discloses new perspectives for further evaluation in the identification local transmission paradigms and initiating effective prevention strategies.
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Affiliation(s)
- Adel Spotin
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Parasitology and Mycology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soheila Rouhani
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Haghighi
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
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3
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Mitochondrial RNA editing in Trypanoplasma borreli: new tools, new revelations. Comput Struct Biotechnol J 2022; 20:6388-6402. [DOI: 10.1016/j.csbj.2022.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
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4
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Gerasimov ES, Gasparyan AA, Afonin DA, Zimmer SL, Kraeva N, Lukeš J, Yurchenko V, Kolesnikov A. Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non-canonical mitochondrial RNA editing events. Nucleic Acids Res 2021; 49:3354-3370. [PMID: 33660779 PMCID: PMC8034629 DOI: 10.1093/nar/gkab114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 01/24/2023] Open
Abstract
Uridine insertion/deletion (U-indel) editing of mitochondrial mRNA, unique to the protistan class Kinetoplastea, generates canonical as well as potentially non-productive editing events. While the molecular machinery and the role of the guide (g) RNAs that provide required information for U-indel editing are well understood, little is known about the forces underlying its apparently error-prone nature. Analysis of a gRNA:mRNA pair allows the dissection of editing events in a given position of a given mitochondrial transcript. A complete gRNA dataset, paired with a fully characterized mRNA population that includes non-canonically edited transcripts, would allow such an analysis to be performed globally across the mitochondrial transcriptome. To achieve this, we have assembled 67 minicircles of the insect parasite Leptomonas pyrrhocoris, with each minicircle typically encoding one gRNA located in one of two similar-sized units of different origin. From this relatively narrow set of annotated gRNAs, we have dissected all identified mitochondrial editing events in L. pyrrhocoris, the strains of which dramatically differ in the abundance of individual minicircle classes. Our results support a model in which a multitude of editing events are driven by a limited set of gRNAs, with individual gRNAs possessing an inherent ability to guide canonical and non-canonical editing.
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Affiliation(s)
- Evgeny S Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow 119435, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Anna A Gasparyan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A Afonin
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow 119435, Russia
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Alexander Kolesnikov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
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Li SJ, Zhang X, Lukeš J, Li BQ, Wang JF, Qu LH, Hide G, Lai DH, Lun ZR. Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen Trypanosoma lewisi. Nucleic Acids Res 2020; 48:9747-9761. [PMID: 32853372 PMCID: PMC7515712 DOI: 10.1093/nar/gkaa700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 08/06/2020] [Accepted: 08/11/2020] [Indexed: 01/01/2023] Open
Abstract
Kinetoplastid flagellates are known for several unusual features, one of which is their complex mitochondrial genome, known as kinetoplast (k) DNA, composed of mutually catenated maxi- and minicircles. Trypanosoma lewisi is a member of the Stercorarian group of trypanosomes which is, based on human infections and experimental data, now considered a zoonotic pathogen. By assembling a total of 58 minicircle classes, which fall into two distinct categories, we describe a novel type of kDNA organization in T. lewisi. RNA-seq approaches allowed us to map the details of uridine insertion and deletion editing events upon the kDNA transcriptome. Moreover, sequencing of small RNA molecules enabled the identification of 169 unique guide (g) RNA genes, with two differently organized minicircle categories both encoding essential gRNAs. The unprecedented organization of minicircles and gRNAs in T. lewisi broadens our knowledge of the structure and expression of the mitochondrial genomes of these human and animal pathogens. Finally, a scenario describing the evolution of minicircles is presented.
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Affiliation(s)
- Su-Jin Li
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, and Key Laboratory of Tropical Diseases Control of the Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Xuan Zhang
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, and Key Laboratory of Tropical Diseases Control of the Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Science, University of South Bohemia, České Budějovice (Budweis) 37005, Czech Republic
| | - Bi-Qi Li
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, and Key Laboratory of Tropical Diseases Control of the Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Ju-Feng Wang
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, and Key Laboratory of Tropical Diseases Control of the Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Geoff Hide
- Ecosystems and Environment Research Centre and Biomedical Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - De-Hua Lai
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, and Key Laboratory of Tropical Diseases Control of the Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Zhao-Rong Lun
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, and Key Laboratory of Tropical Diseases Control of the Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
- Ecosystems and Environment Research Centre and Biomedical Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, UK
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6
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Acunha Escobar T, Dowich G, Cantele LC, Zuravski L, Ferrareze PAG, Duarte CA, Kmetzsch Rosa E Silva L, Lübeck I, Manfredini V. Molecular detection of Leishmania spp. in Brazilian cross-border south region mammalian hosts. Transbound Emerg Dis 2019; 67:476-480. [PMID: 31536676 DOI: 10.1111/tbed.13361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/11/2019] [Accepted: 09/10/2019] [Indexed: 11/30/2022]
Abstract
Visceral leishmaniasis is an endemic zoonotic disease identified especially in developing territories. Brazil's northeast, southeast and midwest have been endemic for several years; currently, the infection is spreading to the south. Dogs are the main reservoirs; however, other mammal species have also been infected. Herein, we have identified the infecting Leishmania species in dogs and horses from the south of Brazil, a new outbreak of the infection. Blood samples were collected in the urban area of Uruguaiana city. DNA was extracted from peripheral blood, kinetoplast DNA (kDNA) and ribosomal DNA (rDNA) fragments were obtained by polymerase chain reaction (PCR) and sequenced. Out of 123 samples, 25 of them (14 dogs and 11 horses) were positive for Leishmania spp. Sequence alignment and phylogenetic analysis revealed that the kDNA in positive samples was similar to four species previously reported: L. infantum/L. chagasi, L. donovani, L. major. Despite kDNA minicircles regions are very useful due to high sensitivity to Leishmania spp. DNA detection, the sequence polymorphism among minicircles can be an obstacle to interspecific differentiation. Our results suggest that these strains are circulating in Brazil south region cross-border and indicate the susceptibility of new outbreak for visceral leishmaniasis infection in horses domiciled in endemic region for canine and human visceral leishmaniasis.
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Affiliation(s)
| | | | | | | | | | | | - Lívia Kmetzsch Rosa E Silva
- Molecular Biology and e Biotechnology, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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Petersen ALDOA, Campos TA, Dantas DADS, Rebouças JDS, da Silva JC, de Menezes JPB, Formiga FR, de Melo JV, Machado G, Veras PST. Encapsulation of the HSP-90 Chaperone Inhibitor 17-AAG in Stable Liposome Allow Increasing the Therapeutic Index as Assessed, in vitro, on Leishmania (L) amazonensis Amastigotes-Hosted in Mouse CBA Macrophages. Front Cell Infect Microbiol 2018; 8:303. [PMID: 30214897 PMCID: PMC6126448 DOI: 10.3389/fcimb.2018.00303] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022] Open
Abstract
The current long-term treatment for leishmaniasis causes severe side effects and resistance in some cases. An evaluation of the anti-leishmanial potential of an HSP90-inhibitor, 17-allylamino-17-demethoxygeldanamycin (17-AAG), demonstrated its potent effect against Leishmania spp. in vitro and in vivo. We have previously shown that 17-AAG can kill L. (L) amazonensis promastigotes with an IC50 of 65 nM and intracellular amastigote at concentrations as low as 125 nM. As this compound presents low solubility and high toxicity in human clinical trials, we prepared an inclusion complex containing hydroxypropyl-β-cyclodextrin and 17-AAG (17-AAG:HPβCD) to improve its solubility. This complex was characterized by scanning electron microscopy, and X-ray diffraction. Liposomes-containing 17-AAG:HPβCD was prepared and evaluated for encapsulation efficiency (EE%), particle size, polydispersity index (PDI), pH, and zeta potential, before and after accelerated and long-term stability testing. An evaluation of leishmanicidal activity against promastigotes and intracellular amastigotes of L. (L) amazonensis was also performed. The characterization techniques utilized confirmed the formation of the inclusion complex, HPβCD:17-AAG, with a resulting 33-fold-enhancement in compound water solubility. Stability studies revealed that 17-AAG:HPβCD-loaded liposomes were smaller than 200 nm, with 99% EE. Stability testing detected no alterations in PDI that was 0.295, pH 7.63, and zeta potential +22.6, suggesting liposome stability, and suitability for evaluating leishmanicidal activity. Treatment of infected macrophages with 0.006 nM of 17-AAG:HPβCD or 17-AAG:HPβCD-loaded liposomes resulted in almost complete amastigote clearance inside macrophages after 48 h. This reduction is similar to the one observed in infected macrophages treated with 2 μM amphotericin B. Our results showed that nanotechnology and drug delivery systems could be used to increase the antileishmanial efficacy and potency of 17-AAG in vitro, while also resulting in reduced toxicity that indicates these formulations may represent a potential therapeutic strategy against leishmaniasis.
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Affiliation(s)
| | - Thiers A Campos
- Graduate Program in Biological Sciences, Center of Biological Sciences, Federal University of Pernambuco, Recife, Brazil.,Laboratory of Electron Microscopy and Microanalysis (LAMM), Center of Strategical Technologies (CETENE), Recife, Brazil
| | | | - Juliana de Souza Rebouças
- Laboratory of Parasite-Host Interaction and Epidemiology (LAIPHE), Gonçalo Moniz Institute-FIOCRUZ, Salvador, Brazil.,Institute of Biological Sciences, University of Pernambuco (UPE), Recife, Brazil
| | - Juliana Cruz da Silva
- Laboratory of Electron Microscopy and Microanalysis (LAMM), Center of Strategical Technologies (CETENE), Recife, Brazil
| | - Juliana P B de Menezes
- Laboratory of Parasite-Host Interaction and Epidemiology (LAIPHE), Gonçalo Moniz Institute-FIOCRUZ, Salvador, Brazil
| | - Fábio R Formiga
- Postgraduate Program in Applied Cellular and Molecular Biology, Institute of Biological Sciences, University of Pernambuco (UPE), Recife, Brazil.,Laboratory of Vector-Borne Infectious Diseases (LEITV), Gonçalo Moniz Institute-FIOCRUZ, Salvador, Brazil
| | - Janaina V de Melo
- Laboratory of Electron Microscopy and Microanalysis (LAMM), Center of Strategical Technologies (CETENE), Recife, Brazil
| | - Giovanna Machado
- Laboratory of Electron Microscopy and Microanalysis (LAMM), Center of Strategical Technologies (CETENE), Recife, Brazil
| | - Patrícia S T Veras
- Laboratory of Parasite-Host Interaction and Epidemiology (LAIPHE), Gonçalo Moniz Institute-FIOCRUZ, Salvador, Brazil.,National Institute of Technology in Tropical Diseases-National Council for Scientific and Technological Development, Brasilia, Brazil
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8
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Gerasimov ES, Gasparyan AA, Litus IA, Logacheva MD, Kolesnikov AA. Minicircle Kinetoplast Genome of Insect Trypanosomatid Leptomonas pyrrhocoris. BIOCHEMISTRY (MOSCOW) 2017; 82:572-578. [PMID: 28601067 DOI: 10.1134/s0006297917050054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We present here the structure of a minicircle population based on transcriptome sequencing of Leptomonas pyrrhocoris. We show that minicircle DNA molecules are dimeric. As in dixenous species, the entire molecule of minicircle DNA is transcribed. This is the first minicircle transcriptome of monoxenous trypanosomatid species determined using NGS technology.
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Affiliation(s)
- E S Gerasimov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
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New Approaches to Systematics of Trypanosomatidae: Criteria for Taxonomic (Re)description. Trends Parasitol 2015; 31:460-469. [PMID: 26433249 DOI: 10.1016/j.pt.2015.06.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 06/09/2015] [Accepted: 06/24/2015] [Indexed: 01/11/2023]
Abstract
While dixenous trypanosomatids represent one of the most dangerous pathogens for humans and domestic animals, their monoxenous relatives have frequently become model organisms for studies of diversity of parasitic protists and host-parasite associations. Yet, the classification of the family Trypanosomatidae is not finalized and often confusing. Here we attempt to make a blueprint for future studies in this field. We would like to elicit a discussion about an updated procedure, as traditional taxonomy was not primarily designed to be used for protists, nor can molecular phylogenetics solve all the problems alone. The current status, specific cases, and examples of generalized solutions are presented under conditions where practicality is openly favored over rigid taxonomic codes or blind phylogenetic approach.
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d’Avila-Levy CM, Boucinha C, Kostygov A, Santos HLC, Morelli KA, Grybchuk-Ieremenko A, Duval L, Votýpka J, Yurchenko V, Grellier P, Lukeš J. Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era. Mem Inst Oswaldo Cruz 2015; 110:956-65. [PMID: 26602872 PMCID: PMC4708014 DOI: 10.1590/0074-02760150253] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/01/2015] [Indexed: 12/12/2022] Open
Abstract
The class Kinetoplastea encompasses both free-living and parasitic species from a wide range of hosts. Several representatives of this group are responsible for severe human diseases and for economic losses in agriculture and livestock. While this group encompasses over 30 genera, most of the available information has been derived from the vertebrate pathogenic genera Leishmaniaand Trypanosoma. Recent studies of the previously neglected groups of Kinetoplastea indicated that the actual diversity is much higher than previously thought. This article discusses the known segment of kinetoplastid diversity and how gene-directed Sanger sequencing and next-generation sequencing methods can help to deepen our knowledge of these interesting protists.
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Affiliation(s)
- Claudia Masini d’Avila-Levy
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Estudos
Integrados em Protozoologia, Coleção de Protozoários, Rio de Janeiro, RJ, Brasil
| | - Carolina Boucinha
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Estudos
Integrados em Protozoologia, Coleção de Protozoários, Rio de Janeiro, RJ, Brasil
| | - Alexei Kostygov
- University of Ostrava, Life Science Research Centre, Ostrava, Czech
Republic
- Russian Academy of Sciences, Zoological Institute, Laboratory of
Molecular Systematics, St Petersburg, Russia
| | - Helena Lúcia Carneiro Santos
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Estudos
Integrados em Protozoologia, Coleção de Protozoários, Rio de Janeiro, RJ, Brasil
| | - Karina Alessandra Morelli
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Estudos
Integrados em Protozoologia, Coleção de Protozoários, Rio de Janeiro, RJ, Brasil
- Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto
Alcântara Gomes, Departamento de Ecologia, Rio de Janeiro, RJ, Brasil
| | | | - Linda Duval
- Sorbonne Universités, Muséum National d’Histoire Naturelle, Centre
National de la Recherche Scientifique, Unité Molécules de Communication et Adaptation
des Microorganisme, Unités Mixte de Recherche 7245, Paris, France
| | - Jan Votýpka
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre,
České Budejovice, Czech Republic
- Charles University, Faculty of Science, Department of Parasitology,
Prague, Czech Republic
| | - Vyacheslav Yurchenko
- University of Ostrava, Life Science Research Centre, Ostrava, Czech
Republic
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre,
České Budejovice, Czech Republic
| | - Philippe Grellier
- Sorbonne Universités, Muséum National d’Histoire Naturelle, Centre
National de la Recherche Scientifique, Unité Molécules de Communication et Adaptation
des Microorganisme, Unités Mixte de Recherche 7245, Paris, France
| | - Julius Lukeš
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre,
České Budejovice, Czech Republic
- University of South Bohemia, Faculty of Sciences, České Budejovice,
Czech Republic
- Canadian Institute for Advanced Research, Toronto, Canada
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11
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Grybchuk-Ieremenko A, Losev A, Kostygov AY, Lukeš J, Yurchenko V. High prevalence of trypanosome co-infections in freshwater fishes. Folia Parasitol (Praha) 2014. [DOI: 10.14411/fp.2014.064] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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12
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The associations of Leishmania major and Leishmania tropica aspects by focusing their morphological and molecular features on clinical appearances in Khuzestan Province, Iran. BIOMED RESEARCH INTERNATIONAL 2014; 2014:913510. [PMID: 25317423 PMCID: PMC4181938 DOI: 10.1155/2014/913510] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/19/2014] [Accepted: 08/27/2014] [Indexed: 11/17/2022]
Abstract
Cutaneous leishmaniasis has various phenotypic aspects consisting of polymorphic amastigotes with different genetic ranges. Samples were collected from suspected patients of Khuzestan province. Prepared smears were stained, scaled, and measured using ocular micrometer. The Cyt b, ITS-rDNA, and microsatellite genes of Leishmania were amplified and Leishmania species were identified by molecular analyses. Of 150 examined suspected patients, 102 were identified to Leishmania species (90 L. major, nine L. tropica, and three unidentified). The amastigotes of 90 L. major had regular and different irregular shapes within three clinical lesions with no and/or low genetic diversity. Three haplotypes of Cyt b of L. major were found but no variation was observed using ITS-rDNA gene. Interesting findings were that all nine L. tropica had regular amastigote shapes with more genetic variations, also a patient which had coinfection of L. major, L. tropica, and Crithidia. At least two L. major and L. tropica were identified in suspected patients of the regions. Different irregular amastigotes' shapes of L. major can be explained by various reservoir hosts and vectors. In contrast, more molecular variations in L. tropica could be justified by genetic characters. Unidentified Leishmania could be mixed pathogens or nonpathogens with mammals' Leishmania or Crithidia.
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Diversity of trypanosomatids (Kinetoplastea: Trypanosomatidae) parasitizing fleas (Insecta: Siphonaptera) and description of a new genus Blechomonas gen. n. Protist 2013; 164:763-81. [PMID: 24113136 DOI: 10.1016/j.protis.2013.08.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/28/2013] [Accepted: 08/30/2013] [Indexed: 11/22/2022]
Abstract
To further investigate the diversity of Trypanosomatidae we have examined the species present within the flea (Siphonaptera) population in the Czech Republic. Out of 1549 fleas, 239 were found to be infected by trypanosomatids. Axenic cultures were established from 90 infected specimens and 29 of them were further characterized. Molecular phylogenetic analysis of the SL RNA, gGAPDH, and SSU rRNA genes revealed a striking diversity within this group and analyzed isolates were classified into 16 Typing units (TUs) of which 15 typified new species. In addition to one Trypanosoma species, two TUs grouped within the sub-family Leishmaniinae, two clustered together with Herpetomonas, wheras 11 TUs formed a novel clade branching off between Trypanosoma spp. and remaining trypanosomatids. We propose to recognize this clade as a new genus Blechomonas and a new subfamily Blechomonadinae, and provide molecular and morphological description of 11 TUs representing this genus. Our finding of such an ancient host-specific group sheds new light at the origin of Trypanosomatidae and the roots of dixenous parasitism. The strict host restriction of Blechomonas to Siphonaptera with adult fleas' dependence on blood meal may reflect passing of parasites from larvae through pupae to adults and implies potential transmission to the warm-blooded vertebrates.
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Oryan A, Shirian S, Tabandeh MR, Hatam GR, Randau G, Daneshbod Y. Genetic diversity of Leishmania major strains isolated from different clinical forms of cutaneous leishmaniasis in southern Iran based on minicircle kDNA. INFECTION GENETICS AND EVOLUTION 2013; 19:226-31. [DOI: 10.1016/j.meegid.2013.07.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/11/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
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Yang BB, Chen DL, Chen JP, Liao L, Hu XS, Xu JN. Analysis of kinetoplast cytochrome b gene of 16 Leishmania isolates from different foci of China: different species of Leishmania in China and their phylogenetic inference. Parasit Vectors 2013; 6:32. [PMID: 23383990 PMCID: PMC3573894 DOI: 10.1186/1756-3305-6-32] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 01/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leishmania species belong to the family Trypanosomatidae and cause leishmaniasis, a geographically widespread disease that infects humans and other vertebrates. This disease remains endemic in China. Due to the large geographic area and complex ecological environment, the taxonomic position and phylogenetic relationship of Chinese Leishmania isolates remain uncertain. A recent internal transcribed spacer 1 and cytochrome oxidase II phylogeny of Chinese Leishmania isolates has challenged some aspects of their traditional taxonomy as well as cladistics hypotheses of their phylogeny. The current study was designed to provide further disease background and sequence analysis. METHODS We systematically analyzed 50 cytochrome b (cyt b) gene sequences of 19 isolates (16 from China, 3 from other countries) sequenced after polymerase chain reaction (PCR) using a special primer for cyt b as well as 31 sequences downloaded from GenBank. After alignment, the data were analyzed using the maximum parsimony, Bayesian and netwok methods. RESULTS Sequences of six haplotypes representing 10 Chinese isolates formed a monophyletic group and clustered with Leishmania tarentolae. The isolates GS1, GS7, XJ771 of this study from China clustered with other isolates of Leishmania donovani complex. The isolate JS1 was a sister to Leishmania tropica, which represented an L. tropica complex instead of clustering with L. donovani complex or with the other 10 Chinese isolates. The isolates KXG-2 and GS-GER20 formed a monophyletic group with Leishmania turanica from central Asia. In the different phylogenetic trees, all of the Chinese isolates occurred in at least four groups regardless of geographic distribution. CONCLUSIONS The undescribed Leishmania species of China, which are clearly causative agents of canine leishmaniasis and human visceral leishmaniasis and are related to Sauroleishmania, may have evolved from a common ancestral parasite that came from the Americas and may have split off earlier than the other old world Leishmania. Our results also suggest the following: the isolates GS7, GS1 and XJ771 occur as part of the L. donovani complex; the JS1 isolate is L. tropica; and the isolate GS-GER20 identified as Leishmania gerbilli is close to KXG-2 which is L. turanica.
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Affiliation(s)
- Bin-Bin Yang
- Department of Medical Laboratory, Weifang Medical University, #7166, The West Baotong street, Weifang, Shandong, 261053, China
- Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, #17, The 3th Section of South Renmin Road, Chengdu, Sichuan, 610041, China
| | - Da-Li Chen
- Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, #17, The 3th Section of South Renmin Road, Chengdu, Sichuan, 610041, China
| | - Jian-Ping Chen
- Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, #17, The 3th Section of South Renmin Road, Chengdu, Sichuan, 610041, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, #24, The South 1st Section of Yihuan Road, Chengdu, Sichuan, 610041, China
| | - Lin Liao
- Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, #17, The 3th Section of South Renmin Road, Chengdu, Sichuan, 610041, China
| | - Xiao-Su Hu
- Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, #17, The 3th Section of South Renmin Road, Chengdu, Sichuan, 610041, China
| | - Jia-Nan Xu
- Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, #17, The 3th Section of South Renmin Road, Chengdu, Sichuan, 610041, China
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Maslov DA, Votýpka J, Yurchenko V, Lukeš J. Diversity and phylogeny of insect trypanosomatids: all that is hidden shall be revealed. Trends Parasitol 2012; 29:43-52. [PMID: 23246083 DOI: 10.1016/j.pt.2012.11.001] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 11/06/2012] [Accepted: 11/08/2012] [Indexed: 10/27/2022]
Abstract
Monoxenous trypanosomatids, which are usually regarded as benign dwellers of the insect alimentary tract, represent a relatively obscure group within the family Trypanosomatidae. This field of study has long been in disarray with the genus level taxonomy of this group remaining artificial, species criteria elusive, host specificity and occurrence poorly known, and their diversity mostly unexplored. The time has arrived to remedy this situation: a phylogenetic approach has been applied to taxa recognition and description, and a culture-independent (PCR-based) approach for detection and identification of organisms in nature has made it feasible to study the diversity of the group. Although more than 100 typing units have been discovered recently, these appear to represent a small segment of trypanosomatid biodiversity, which still remains to be uncovered.
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Affiliation(s)
- Dmitri A Maslov
- Department of Biology, University of California, Riverside, CA 92521, USA.
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Molecular approaches for a better understanding of the epidemiology and population genetics ofLeishmania. Parasitology 2010; 138:405-25. [DOI: 10.1017/s0031182010001538] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
SUMMARYMolecular approaches are being used increasingly for epidemiological studies of visceral and cutaneous leishmaniases. Several molecular markers resolving genetic differences betweenLeishmaniaparasites at species and strain levels have been developed to address key epidemiological and population genetic questions. The current gold standard, multilocus enzyme typing (MLEE), needs cultured parasites and lacks discriminatory power. PCR assays identifying species directly with clinical samples have proven useful in numerous field studies. Multilocus sequence typing (MLST) is potentially the most powerful phylogenetic approach and will, most probably, replace MLEE in the future. Multilocus microsatellite typing (MLMT) is able to discriminate below the zymodeme level and seems to be the best candidate for becoming the gold standard for distinction of strains. Population genetic studies by MLMT revealed geographical and hierarchic population structure inL. tropica, L. majorand theL. donovanicomplex. The existence of hybrids and gene flow betweenLeishmaniapopulations suggests that sexual recombination is more frequent than previously thought. However, typing and analytical tools need to be further improved. Accessible databases should be created and sustained for integrating data obtained by different researchers. This would allow for global analyses and help to avoid biases in analyses due to small sample sizes.
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Yatawara L, Wickramasinghe S, Rajapakse RPVJ, Siyambalagoda RRMLR, Le TH, Watanabe Y, Agatsuma T. Morphological and molecular studies on Sri Lankan Leishmania. Trop Med Health 2008. [DOI: 10.2149/tmh.2008-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Sturm NR, Dollet M, Lukes J, Campbell DA. Rational sub-division of plant trypanosomes (Phytomonas spp.) based on minicircle conserved region analysis. INFECTION GENETICS AND EVOLUTION 2007; 7:570-6. [PMID: 17499027 DOI: 10.1016/j.meegid.2007.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Revised: 04/04/2007] [Accepted: 04/05/2007] [Indexed: 10/23/2022]
Abstract
The sequences of minicircle conserved regions from various plant trypanosomatids have been determined and analyzed. The goal of this study was to add another tool to the arsenal of molecular probes for distinguishing between the different trypanosomatids occurring in plants: systemic trypanosomatids multiplying in the sap, those from the laticiferous tubes, and those developing in fruits, seeds or flowers but not in the plant itself and that are frequently considered as opportunistic insect trypanosomatids. As some plant intraphloemic trypanosomatids are the causative agents of important diseases, a clear definition of the different types of trypanosomatids is critical. The conserved region of the mitochondrial minicircle provides several specific features in a small sequence region containing three functionally elements required for minicircle replication. Trees generated from the analysis recapitulated trees drawn from analyses of isoenzymes, RAPD, and particular gene sequences, supporting the validity of the small region used in this work. Three groups of isolates were significant and in accordance with previous work. The peculiarity of phloem-restricted trypanosomatids associated with wilts of coconut and oil palm in Latin America - group H - is confirmed. In agreement with previous studies on their biological and serological properties the results highlighted this group called 'phloemicola'. It always differentiated from all other latex and fruit isolates or opportunistic trypanosomatids, like insect trypanosomatids. We can assert that phloemicola is the only well-defined taxon among all plant trypanosomatids. A group of non-pathogenic latex isolates from South American euphorbs (G), and a heterogenous group (A) including one fruit, one possible latex and one insect isolate are clearly distinct groups. The group of Mediterranean isolates from latex (D), even with a low boostrap, stood out well from other groups. The remainder of the isolates fell into a heterogeneous cluster. At least eight different groups in the plant trypanosomatids were identified.
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Affiliation(s)
- Nancy R Sturm
- CIRAD,UPR29 Etiologie Dépérissements, Département Systèmes Biologiques, TA A-29/F, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
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Luyo-Acero GE, Uezato H, Oshiro M, Takei K, Kariya K, Katakura K, Gomez-Landires E, Hashiguchi Y, Nonaka S. Sequence variation of the cytochrome b gene of various human infecting members of the genus Leishmania and their phylogeny. Parasitology 2004; 128:483-91. [PMID: 15180316 DOI: 10.1017/s0031182004004792] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Cytochrome b (Cyt b) gene has proved to be useful for identification and classification of many mammals and plants. In order to evaluate the utility of this gene for discrimination of Leishmania parasites as well as for exploring their phylogenetic relationships, we determined the nucleotide sequences of the Cyt b gene from 13 human-infecting Leishmania species (14 strains) from the New and Old Worlds. The Cyt b genes, approximately 1080 base pairs, were found to be A/T rich, and their 5' terminal-editing regions were highly conserved. The nucleotide sequence variation among them was enough to discriminate parasite species; 245 nucleotide positions were polymorphic and 190 positions were parsimony informative. The phylogenetic relationships based on this gene, showed good agreement with the classification of Lainson & Shaw (1987) except for the inclusion of L. (L.) major in the L. (L.) tropica complex and the placement of L. tarentolae in another genus. These data show that the Cyt b gene is useful for phylogenetic study of Leishmania parasites.
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Affiliation(s)
- G E Luyo-Acero
- Department of Dermatology, Faculty of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa 903-0125, Japan
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Martin DS, Wright ADG, Barta JR, Desser SS. Phylogenetic position of the giant anuran trypanosomes Trypanosoma chattoni, Trypanosoma fallisi, Trypanosoma mega, Trypanosoma neveulemairei, and Trypanosoma ranarum inferred from 18S rRNA gene sequences. J Parasitol 2002; 88:566-71. [PMID: 12099428 DOI: 10.1645/0022-3395(2002)088[0566:ppotga]2.0.co;2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Phylogenetic relationships within the kinetoplastid flagellates were inferred from comparisons of small-subunit ribosomal RNA gene sequences. These included 5 new gene sequences, Trypanosoma fallisi (2,239 bp), Trypanosoma chattoni (2,180 bp), Trypanosoma mega (2,211 bp), Trypanosoma neveulemairei (2,197 bp), and Trypanosoma ranarum (2,203 bp). Trees produced using maximum-parsimony and distance-matrix methods (least-squares, neighbor-joining, and maximum-likelihood), supported by strong bootstrap and quartet-puzzle analyses, indicated that the trypanosomes are a monophyletic group that divides into 2 major lineages, the salivarian trypanosomes and the nonsalivarian trypanosomes. The nonsalivarian trypanosomes further divide into 2 lineages, 1 containing trypanosomes of birds, mammals, and reptiles and the other containing trypanosomes of fish, reptiles, and anurans. Among the giant trypanosomes, T. chattoni is clearly shown to be distantly related to all the other anuran trypanosome species. Trypanosoma mega is closely associated with T. fallisi and T. ranarum, whereas T. neveulemairei and Trypanosoma rotatorium are sister taxa. The branching order of the anuran trypanosomes suggests that some toad trypanosomes may have evolved by host switching from frogs to toads.
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Affiliation(s)
- Donald S Martin
- Parasitology Laboratory, Ontario Ministry of Health and Long-Term Care, Etobicoke, Canada.
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Dollet M, Sturm NR, Ahomadegbe JC, Campbell DA. Kinetoplast DNA minicircles of phloem-restricted Phytomonas associated with wilt diseases of coconut and oil palms have a two-domain structure. FEMS Microbiol Lett 2001; 205:65-9. [PMID: 11728717 DOI: 10.1111/j.1574-6968.2001.tb10926.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We report the cloning and sequencing of the first minicircle from a phloem-restricted, pathogenic Phytomonas sp. (Hart 1) isolated from a coconut palm with hartrot disease. The minicircle possessed a two-domain structure of two conserved regions, each containing three conserved sequence blocks (CSB). Based on the sequence around CSB 3 from Hart 1, PCR primers were designed to allow specific amplification of Phytomonas minicircles. This primer pair demonstrated specificity for at least six groups of plant trypanosomatids and did not amplify from insect trypanosomatids. The PCR results were consistent with a two-domain structure for other plant trypanosomatids.
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Affiliation(s)
- M Dollet
- CIRAD, TA 30/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.
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Abstract
Trypanosomatids have been traditionally allocated to a number of genera that were described based on morphological features and host range. Recently molecular studies have provided new data that has allowed a reexamination of the genera. While in some cases the molecular data has been in agreement with the morphological characters they have also reinforced existing doubts about some current generic divisions as well as raising new concerns. A revision of the trypanosomatid genera is required. Suggested features of such a revision would include: (1) The possible division of Trypanosoma into new genera to reflect the wide genetic diversity of this group; (2) The inclusion of Leishmania, Sauroleishmania and Endotrypanum within a single genus given their high genetic affinity; (3) The complete revision of the monogenetic typanosomatid genera to reflect monophyletic groups; (4) A more precise redescription of Phytomonas so as to only include the monophyletic plant flagellates.
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Affiliation(s)
- H Momen
- Instituto Oswaldo Cruz, Fiocruz, Avenue Brasil 4365, 21045-900, Rio de Janeiro, Brazil.
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Addendum. ADVANCES IN PARASITOLOGY 2001. [DOI: 10.1016/s0065-308x(01)48004-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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