Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17:333–51.
Article
CAS
Google Scholar
Li H, Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. 2010;26:589–95.
Article
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
Article
Google Scholar
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–8.
Article
CAS
Google Scholar
Cameron DL, Di Stefano L, Papenfuss AT. Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software. Nat Commun. 2019. https://doi.org/10.1038/s41467-019-11146-4.
Article
PubMed
PubMed Central
Google Scholar
Hahn C, Bachmann L, Chevreux B. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Res. 2013;41:e129–e129.
Article
CAS
Google Scholar
Dierckxsens N, Mardulyn P, Smits G. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2017;45:e18.
Article
Google Scholar
Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, et al. The genome of the African trypanosome Trypanosoma brucei. Science. 2005;309:416–22.
Article
CAS
Google Scholar
Peacock CS, Seeger K, Harris D, Murphy L, Ruiz JC, Quail MA, et al. Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat Genet. 2007. https://doi.org/10.1038/ng2053.
Article
PubMed
PubMed Central
Google Scholar
Tihon E, Imamura H, Van den Broeck F, Vermeiren L, Dujardin J-C, Van Den Abbeele J. Genomic analysis of isometamidium chloride resistance in Trypanosoma congolense. Int J Parasitol Drugs Drug Resist. 2017;7:350–61.
Article
Google Scholar
Cuypers B, Lecordier L, Meehan CJ, Van den Broeck F, Imamura H, Büscher P, et al. Apolipoprotein L1 variant associated with increased susceptibility to trypanosome infection. MBio. 2016. https://doi.org/10.1128/mBio.02198-15.
Article
PubMed
PubMed Central
Google Scholar
Cuypers B, Van den Broeck F, Van Reet N, Meehan CJ, Cauchard J, Wilkes JM, et al. Genome-wide SNP analysis reveals distinct origins of Trypanosoma evansi and Trypanosoma equiperdum. Genome Biol Evol. 2017;9:1990–7.
Article
CAS
Google Scholar
Domagalska MA, Imamura H, Sanders M, Van den Broeck F, Bhattarai NR, Vanaerschot M, et al. Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent. PLoS Negl Trop Dis. 2019;13:e0007900.
Article
Google Scholar
Rogers MB, Downing T, Smith BA, Imamura H, Sanders M, Svobodova M, et al. Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated leishmania population. PLoS Genet. 2014. https://doi.org/10.1371/journal.pgen.1004092.
Article
PubMed
PubMed Central
Google Scholar
Tihon E, Imamura H, Dujardin J-C, Van Den Abbeele J, Van den Broeck F. Discovery and genomic analyses of hybridization between divergent lineages of Trypanosoma congolense, causative agent of Animal African trypanosomiasis. Mol Ecol. 2017. https://doi.org/10.1111/mec.14271.
Article
PubMed
Google Scholar
Van den Broeck F, Tavernier LJM, Vermeiren L, Dujardin JC, Van Den Abbeele J. Mitonuclear genomics challenges the theory of clonality in Trypanosoma congolense: reply to Tibayrenc and Ayala. Mol Ecol. 2018. https://doi.org/10.1111/mec.14809.
Article
PubMed
Google Scholar
Schwabl P, Imamura H, Van den Broeck F, Costales JA, Maiguashca-Sánchez J, Miles MA, et al. Meiotic sex in Chagas disease parasite Trypanosoma cruzi. Nat Commun. 2019. https://doi.org/10.1038/s41467-019-11771-z.
Article
PubMed
PubMed Central
Google Scholar
Inbar E, Shaik J, Iantorno SA, Romano A, Nzelu CO, Owens K, et al. Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in leishmania. PLoS Genet. 2019;15:1–28.
Article
Google Scholar
Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S, Sundar S, et al. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. Elife. 2016. https://doi.org/10.7554/eLife.12613.
Article
PubMed
PubMed Central
Google Scholar
Franssen SU, Durrant C, Stark O, Moser B, Downing T, Imamura H, et al. Global genome diversity of the Leishmania donovani complex. Elife. 2020;9:e51243.
Article
CAS
Google Scholar
Van den Broeck F, Savill NJ, Imamura H, Sanders M, Maes I, Cooper S, et al. Ecological divergence and hybridization of neotropical Leishmania parasites. Proc Natl Acad Sci USA. 2020. https://doi.org/10.1073/pnas.1920136117.
Article
PubMed
PubMed Central
Google Scholar
Lukes J, Guilbride DL, Votýpka J, Zíková A, Benne R, Englund PT, et al. Kinetoplast DNA network : evolution of an Improbable structure. Eukaryot Cell. 2002;1:495–502.
Article
CAS
Google Scholar
Koslowsky D, Sun Y, Hindenach J, Theisen T, Lucas J. The insect-phase gRNA transcriptome in Trypanosoma brucei. Nucleic Acids Res. 2014. https://doi.org/10.1093/nar/gkt973.
Article
PubMed
Google Scholar
Cooper S, Wadsworth ES, Ochsenreiter T, Ivens A, Savill NJ, Schnaufer A. Assembly and annotation of the mitochondrial minicircle genome of a differentiation-competent strain of Trypanosoma brucei. Nucleic Acids Res. 2019;47:11304–25.
Article
CAS
Google Scholar
Wu J, Liu B, Cheng F, Ramchiary N, Choi SR, Lim YP, et al. Sequencing of chloroplast genome using whole cellular DNA and solexa sequencing technology. Front Plant Sci. 2012;3:243.
CAS
PubMed
PubMed Central
Google Scholar
Simpson L, Douglass SM, Lake JA, Pellegrini M, Li F. Comparison of the mitochondrial genomes and steady state transcriptomes of two strains of the trypanosomatid parasite, leishmania tarentolae. PLoS Negl Trop Dis. 2015;9:e0003841.
Article
Google Scholar
Gerasimov ES, Gasparyan AA, Afonin DA, Zimmer SL, Kraeva N, Lukeš J, et al. Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non-canonical mitochondrial RNA editing events. Nucleic Acids Res. 2021;49:3354–70.
Article
CAS
Google Scholar
Gerasimov ES, Gasparyan AA, Litus IA, Logacheva MD, Kolesnikov AA. Minicircle kinetoplast genome of insect trypanosomatid leptomonas pyrrhocoris. Biochemistry. 2017;82:572–8.
CAS
PubMed
Google Scholar
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9.
Article
CAS
Google Scholar
Jørgensen TS, Xu Z, Hansen MA, Sørensen SJ, Hansen LH. Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome. PLoS ONE. 2014;9:e87924.
Article
Google Scholar
Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015. https://doi.org/10.1093/bioinformatics/btv033.
Article
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Article
CAS
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Article
CAS
Google Scholar
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: A versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.
Article
Google Scholar
Ginestet C. Ggplot2: elegant graphics for data analysis: book reviews. J R Stat Soc Ser A Stat Soc. 2011;174:245–6.
Article
Google Scholar
Lin R-H, Lai D-H, Zheng L-L, Wu J, Lukeš J, Hide G, et al. Analysis of the mitochondrial maxicircle of Trypanosoma lewisi, a neglected human pathogen. Parasites Vectors. 2015. https://doi.org/10.1186/s13071-015-1281-8.
Article
PubMed
PubMed Central
Google Scholar
Lai D-H, Hashimi H, Lun Z-R, Ayala FJ, Lukes J. Adaptations of Trypanosoma brucei to gradual loss of kinetoplast DNA: Trypanosoma equiperdum and Trypanosoma evansi are petite mutants of T. brucei. Proc Natl Acad Sci USA. 2008;105:1999–2004.
Article
CAS
Google Scholar
Otto TD, Dillon GP, Degrave WS, Berriman M. RATT: rapid annotation transfer tool. Nucleic Acids Res. 2011;39:e87.
Article
Google Scholar
Ray DS. Conserved sequence blocks in kinetoplast minicircles from diverse species of trypanosomes. Mol Cell Biol. 1989;9:1365–7.
CAS
PubMed
PubMed Central
Google Scholar
Bailey TL, Johnson J, Grant CE, Noble WS. The MEME suite. Nucleic Acids Res. 2015;43:W39-49.
Article
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
Google Scholar
Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.
Article
Google Scholar
d’Avila-Levy CM, Boucinha C, Kostygov A, Santos HLC, Morelli KA, Grybchuk-Ieremenko A, et al. Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era. Mem Inst Oswaldo Cruz. 2015;110:956–65.
Article
Google Scholar