Open Access
| Issue |
Parasite
Volume 33, 2026
|
|
|---|---|---|
| Article Number | 34 | |
| Number of page(s) | 11 | |
| DOI | https://doi.org/10.1051/parasite/2026034 | |
| Published online | 03 June 2026 | |
- Alvarenga JSC, Ligeiro CM, Gontijo CMF, Cortes S, Campino L, Vago AR, Melo MN. 2012. KDNA genetic signatures obtained by LSSP-PCR analysis of Leishmania (Leishmania) infantum isolated from the new and the old world. PLoS One, 7, e43363. [Google Scholar]
- Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120. [CrossRef] [PubMed] [Google Scholar]
- Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu Y-X, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, Hooft JJJ van der, Vargas F, Vázquez-Baeza Y, Vogtmann E, Caporaso JG. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 852–857. [CrossRef] [PubMed] [Google Scholar]
- Botero A, Kapeller I, Cooper C, Clode PL, Shlomai J, Thompson RCA. 2018. The kinetoplast DNA of the Australian trypanosome, Trypanosoma copemani, shares features with Trypanosoma cruzi and Trypanosoma lewisi. International Journal for Parasitology, 48, 691–700. [Google Scholar]
- Brewster S, Barker DC. 2002. Analysis of minicircle classes in Leishmania (Viannia) species. Transactions of the Royal Society of Tropical Medicine and Hygiene, 96 Suppl 1, S55–63. [Google Scholar]
- Bruijn MH de, Barker DC. 1992. Diagnosis of New World leishmaniasis: specific detection of species of the Leishmania braziliensis complex by amplification of kinetoplast DNA. Acta Tropica, 52, 45–58. [Google Scholar]
- Callejas-Hernández F, Herreros-Cabello A, Del Moral-Salmoral J, Fresno M, Gironès N. 2021. The complete mitochondrial DNA of Trypanosoma cruzi: Maxicircles and minicircles. Frontiers in Cellular and Infection Microbiology, 11, 672448. [Google Scholar]
- Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics, 10, 421. [Google Scholar]
- Camacho E, Rastrojo A, Sanchiz Á, González-de la Fuente S, Aguado B, Requena JM. 2019. Leishmania mitochondrial genomes: maxicircle structure and heterogeneity of minicircles. Genes, 10, 758. [Google Scholar]
- Ceccarelli M, Buffi G, Diotallevi A, Andreoni F, Bencardino D, Vitale F, Castelli G, Bruno F, Magnani M, Galluzzi L. 2020. Evaluation of a kDNA-Based qPCR assay for the detection and quantification of Old World Leishmania species. Microorganisms, 8, 2006. [Google Scholar]
- Cooper S, Wadsworth ES, Ochsenreiter T, Ivens A, Savill NJ, Schnaufer A. 2019. Assembly and annotation of the mitochondrial minicircle genome of a differentiation-competent strain of Trypanosoma brucei. Nucleic Acids Research, 47, 11304–11325. [Google Scholar]
- Cooper S, Wadsworth ES, Schnaufer A, Savill NJ. 2022. Organization of minicircle cassettes and guide RNA genes in Trypanosoma brucei. RNA (New York), 28, 972–992. [Google Scholar]
- Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. 2021. Twelve years of SAMtools and BCFtools. GigaScience, 10, giab008. [Google Scholar]
- De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. 2018. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34, 2666–2669. [CrossRef] [PubMed] [Google Scholar]
- Degrave W, Fragoso SP, Britto C, Heuverswyn H van, Kidane GZ, Cardoso MA, Mueller RU, Simpson L, Morel CM. 1988. Peculiar sequence organization of kinetoplast DNA minicircles from Trypanosoma cruzi. Molecular and Biochemical Parasitology, 27, 63–70. [Google Scholar]
- Díaz AG, Ragone PG, Rusman F, Floridia-Yapur N, Barquez RM, Díaz MM, Tomasini N, Diosque P. 2020. A novel genotype and first record of Trypanosoma lainsoni in Argentina. Pathogens, 9, 731. [Google Scholar]
- Ferreira GA, Soares FCS, Vasconcellos SA, Rodrigues EHG, Werkhäuser RP, Brito MEF de, Abath FGC. 2007. Discrimination of Leishmania braziliensis variants by kDNA signatures produced by LSSP-PCR. Journal of Parasitology, 93, 712–714. [Google Scholar]
- Geerts M, Schnaufer A, Van den Broeck F. 2021. rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects. BMC Bioinformatics, 22, 468. [Google Scholar]
- Gómez-Palacio A, Cruz-Saavedra L, Van den Broeck F, Geerts M, Pita S, Vallejo GA, Carranza C, Ramírez JD. 2024. High-throughput analysis of the Trypanosoma cruzi minicirculome (mcDNA) unveils structural variation and functional diversity. Scientific Reports, 14, 5578. [Google Scholar]
- Hong M, Simpson L. 2003. Genomic organization of Trypanosoma brucei kinetoplast DNA minicircles. Protist, 154, 265–279. [Google Scholar]
- Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR. 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biology, 16, 294. [Google Scholar]
- Jensen RE, Englund PT. 2012. Network news: the replication of kinetoplast DNA. Annual Review of Microbiology, 66, 473–491. [Google Scholar]
- Kaufer A, Stark D, Ellis J. 2019. Evolutionary insight into the Trypanosomatidae using alignment-free phylogenomics of the kinetoplast. Pathogens, 8, 157. [Google Scholar]
- Kidane GZ, Hughes D, Simpson L. 1984. Sequence heterogeneity and anomalous electrophoretic mobility of kinetoplast minicircle DNA from Leishmania tarentolae. Gene, 27, 265–277. [Google Scholar]
- Li S-J, Zhang X, Lukeš J, Li B-Q, Wang J-F, Qu L-H, Hide G, Lai D-H, Lun Z-R. 2020. Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen Trypanosoma lewisi. Nucleic Acids Research, 48, 9747–9761. [Google Scholar]
- Lukes J, Guilbride DL, Votýpka J, Zíková A, Benne R, Englund PT. 2002. Kinetoplast DNA network: evolution of an improbable structure. Eukaryotic Cell, 1, 495–502. [Google Scholar]
- Lukes J, Hashimi H, Zíková A. 2005. Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Current Genetics, 48, 277–299. [Google Scholar]
- Naiff RD, Barrett TV. 2013. Trypanosoma (Megatrypanum) lainsoni n. sp. from Mesomys hispidus (Rodentia: Echimyidae) in Brazil: trypomastigotes described from experimentally infected laboratory mice. Parasite, 20, 51. [Google Scholar]
- Nantes WAG, Santos FM, Macedo GC de, Barreto WTG, Gonçalves LR, Rodrigues MS, Chulli JVM, Rucco AC, Assis W de O, Porfírio GE de O, Oliveira CE de, Xavier SC das C, Herrera HM, Jansen AM. 2021. Trypanosomatid species in Didelphis albiventris from urban forest fragments. Parasitology Research, 120, 223–231. [Google Scholar]
- Oliveira MM de, Ferrando CPR, Gómez-Hernández C, Oliveira KR de, Araújo IAC, Ribeiro PVA, Mineo TWP, Leiner NO, Mineo JR, Silva SM da. 2023. Prevalence of Trypanosoma lainsoni and its effects of parasitism on the health of non-volant small mammals from the Brazilian Cerrado. Parasitology Research, 122, 1509–1518. [Google Scholar]
- Ortiz PA, Garcia HA, Lima L, Silva FM da, Campaner M, Pereira CL, Jittapalapong S, Neves L, Desquesnes M, Camargo EP, Teixeira MMG. 2018. Diagnosis and genetic analysis of the worldwide distributed Rattus-borne Trypanosoma (Herpetosoma) lewisi and its allied species in blood and fleas of rodents. Infection, Genetics and Evolution, 63, 380–390. [Google Scholar]
- Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841–842. [Google Scholar]
- Ray DS. 1989. Conserved sequence blocks in kinetoplast minicircles from diverse species of trypanosomes. Molecular and Cellular Biology, 9, 1365–1367. [Google Scholar]
- Rodrigues MS, Lima L, Xavier SC das C, Herrera HM, Rocha FL, Roque ALR, Teixeira MMG, Jansen AM. 2019. Uncovering Trypanosoma spp. diversity of wild mammals by the use of DNA from blood clots. International Journal for Parasitology. Parasites and Wildlife, 8, 171–181. [Google Scholar]
- Rusman F, Aramayo V, Floridia-Yapur N, Díaz AG, Ponce T, Hodi S, Aguirre JJ, Greif G, Berná L, Robello C, Diosque P, Tomasini N. 2025. Comparative maxicircle analysis in Trypanosoma species from the LSRM clade highlights patterns in an underexplored lineage. PLoS One, 20, e0332749. [Google Scholar]
- Rusman F, Díaz AG, Ponce T, Floridia-Yapur N, Barnabé C, Diosque P, Tomasini N. 2023. Wide reference databases for typing Trypanosoma cruzi based on amplicon sequencing of the minicircle hypervariable region. PLoS Neglected Tropical Diseases, 17, e0011764. [Google Scholar]
- Rusman F, Floridia-Yapur N, Tomasini N, Diosque P. 2021. Guide RNA repertoires in the main lineages of Trypanosoma cruzi: High diversity and variable redundancy among strains. Frontiers in Cellular and Infection Microbiology, 11, 663416. [Google Scholar]
- Rusman F, Tomasini N, Yapur N-F, Puebla AF, Ragone PG, Diosque P. 2019. Elucidating diversity in the class composition of the minicircle hypervariable region of Trypanosoma cruzi: New perspectives on typing and kDNA inheritance. PLoS Neglected Tropical Diseases, 13, e0007536. [Google Scholar]
- Santos FM, Sano NY, Liberal SC, Dario MA, Nantes WAG, Alves FM, Silva AR da, De Oliveira CE, Roque ALR, Herrera HM, Jansen AM. 2022. Kinetoplastid species maintained by a small mammal community in the pantanal biome. Pathogens, 11, 1205. [Google Scholar]
- Selvapandiyan A, Duncan R, Mendez J, Kumar R, Salotra P, Cardo LJ, Nakhasi HL. 2008. A Leishmania minicircle DNA footprint assay for sensitive detection and rapid speciation of clinical isolates. Transfusion, 48, 1787–1798. [Google Scholar]
- Simpson L, Thiemann OH, Savill NJ, Alfonzo JD, Maslov DA. 2000. Evolution of RNA editing in trypanosome mitochondria. Proceedings of the National Academy of Sciences of the United States of America, 97, 6986–6993. [Google Scholar]
- Simpson L, Douglass SM, Lake JA, Pellegrini M, Li F. 2015. Comparison of the mitochondrial genomes and steady state transcriptomes of two strains of the trypanosomatid parasite, Leishmania tarentolae. PLoS Neglected Tropical Diseases, 9, e0003841. [Google Scholar]
- Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution, 38, 3022–3027. [CrossRef] [PubMed] [Google Scholar]
- Telleria J, Lafay B, Virreira M, Barnabé C, Tibayrenc M, Svoboda M. 2006. Trypanosoma cruzi: sequence analysis of the variable region of kinetoplast minicircles. Experimental Parasitology, 114, 279–288. [Google Scholar]
- Thorvaldsdóttir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics, 14, 178–192. [CrossRef] [PubMed] [Google Scholar]
- Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. 2012. Primer3 – new capabilities and interfaces. Nucleic Acids Research, 40, e115. [Google Scholar]
- Vallejo GA, Macedo AM, Chiari E, Pena SD. 1994. Kinetoplast DNA from Trypanosoma rangeli contains two distinct classes of minicircles with different size and molecular organization. Molecular and Biochemical Parasitology, 67, 245–253. [Google Scholar]
- Van den Broeck F, Savill NJ, Imamura H, Sanders M, Maes I, Cooper S, Mateus D, Jara M, Adaui V, Arevalo J, Llanos-Cuentas A, Garcia L, Cupolillo E, Miles M, Berriman M, Schnaufer A, Cotton JA, Dujardin J-C. 2020. Ecological divergence and hybridization of Neotropical Leishmania parasites. Proceedings of the National Academy of Sciences of the United States of America, 117, 25159–25168. [Google Scholar]
- Vasimuddin Md, Misra S, Li H, Aluru S. 2019. Efficient architecture-aware acceleration of BWA-MEM for multicore systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). pp. 314–324. [Google Scholar]
- Veas F, Cuny G, Brenière SF, Tibayrenc M. 1990. Subspecific kDNA probes for major clones of Trypanosoma cruzi. Acta Tropica, 48, 79–82. [Google Scholar]
- Wick RR, Holt KE. 2022. Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLoS Computational Biology, 18, e1009802. [Google Scholar]
- Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. 2012. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics, 13, 134. [CrossRef] [PubMed] [Google Scholar]
Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.
Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.
Initial download of the metrics may take a while.
