While numerous genomes of Leishmania spp. have been sequenced and analyzed, an understanding of the evolutionary history of these organisms remains limited due to the unavailability of the sequence data for their closest known relatives, Endotrypanum and Porcisia spp., infecting sloths and porcupines. We have sequenced and analyzed genomes of three members of this clade in order to fill this gap. Their comparative analyses revealed only minute differences from Leishmaniamajor genome in terms of metabolic capacities. We also documented that the number of genes under positive selection on the Endotrypanum/Porcisia branch is rather small, with the flagellum-related group of genes being over-represented. Most significantly, the analysis of gene family evolution revealed a substantially reduced repertoire of surface proteins, such as amastins and biopterin transporters BT1 in the Endotrypanum/Porcisia species when compared to amastigote-dwelling Leishmania. This reduction was especially pronounced for δ-amastins, a subfamily of cell surface proteins crucial in the propagation of Leishmania amastigotes inside vertebrate macrophages and, apparently, dispensable for Endotrypanum/Porcisia, which do not infect such cells.

Biomedical Institute São Paulo University São Paulo 05508 Brazil

Department of Parasitology Faculty of Science Charles University 12844 Prague Czech Republic

e Duve Institute Université Catholique de Louvain 1200 Brussels Belgium

Faculty of Biology M 5 Lomonosov Moscow State University 119991 Moscow Russia

Faculty of Science University of South Bohemia 37005 České Budějovice Czech Republic

Institute of Parasitology Biology Centre Czech Academy of Sciences 37005 České Budějovice Czech Republic

Life Science Research Centre Faculty of Science University of Ostrava 71000 Ostrava Czech Republic

Martsinovsky Institute of Medical Parasitology Tropical and Vector Borne Diseases Sechenov University 119435 Moscow Russia

Zoological Institute of the Russian Academy of Sciences 199034 St Petersburg Russia

Zobrazit více v PubMed

Maslov D.A., Opperdoes F.R., Kostygov A.Y., Hashimi H., Lukeš J., Yurchenko V. Recent advances in trypanosomatid research: Genome organization, expression, metabolism, taxonomy and evolution. Parasitology. 2019;146:1–27. doi: 10.1017/S0031182018000951. PubMed DOI

Lukeš J., Butenko A., Hashimi H., Maslov D.A., Votýpka J., Yurchenko V. Trypanosomatids are much more than just trypanosomes: Clues from the expanded family tree. Trends Parasitol. 2018;34:466–480. doi: 10.1016/j.pt.2018.03.002. PubMed DOI

Lukeš J., Skalický T., Týč J., Votýpka J., Yurchenko V. Evolution of parasitism in kinetoplastid flagellates. Mol. Biochem. Parasitol. 2014;195:115–122. doi: 10.1016/j.molbiopara.2014.05.007. PubMed DOI

Kostygov A.Y., Yurchenko V. Revised classification of the subfamily Leishmaniinae (Trypanosomatidae) Folia Parasitol. 2017;64:020. doi: 10.14411/fp.2017.020. PubMed DOI

Jirků M., Yurchenko V., Lukeš J., Maslov D.A. New species of insect trypanosomatids from Costa Rica and the proposal for a new subfamily within the Trypanosomatidae. J. Eukaryot. Microbiol. 2012;59:537–547. doi: 10.1111/j.1550-7408.2012.00636.x. PubMed DOI

Bruschi F., Gradoni L. The Leishmaniases: Old Neglected Tropical Diseases. Springer; Cham, Switzerland: 2018. p. 245. DOI

Akhoundi M., Downing T., Votýpka J., Kuhls K., Lukeš J., Cannet A., Ravel C., Marty P., Delaunay P., Kasbari M., et al. Leishmania infections: Molecular targets and diagnosis. Mol. Asp. Med. 2017;57:1–29. doi: 10.1016/j.mam.2016.11.012. PubMed DOI

Espinosa O.A., Serrano M.G., Camargo E.P., Teixeira M.M., Shaw J.J. An appraisal of the taxonomy and nomenclature of trypanosomatids presently classified as Leishmania and Endotrypanum. Parasitology. 2018;145:430–442. doi: 10.1017/S0031182016002092. PubMed DOI

Butenko A., Kostygov A.Y., Sádlová J., Kleschenko Y., Bečvář T., Podešvová L., Macedo D.H., Žihala D., Lukeš J., Bates P.A., et al. Comparative genomics of Leishmania (Mundinia) BMC Genom. 2019;20:726. doi: 10.1186/s12864-019-6126-y. PubMed DOI PMC

Coughlan S., Taylor A.S., Feane E., Sanders M., Schonian G., Cotton J.A., Downing T. Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus. R. Soc. Open Sci. 2018;5:172212. doi: 10.1098/rsos.172212. PubMed DOI PMC

Coughlan S., Mulhair P., Sanders M., Schonian G., Cotton J.A., Downing T. The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania. Sci. Rep. 2017;7:43747. doi: 10.1038/srep43747. PubMed DOI PMC

Valdivia H.O., Reis-Cunha J.L., Rodrigues-Luiz G.F., Baptista R.P., Baldeviano G.C., Gerbasi R.V., Dobson D.E., Pratlong F., Bastien P., Lescano A.G., et al. Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis. BMC Genom. 2015;16:715. doi: 10.1186/s12864-015-1928-z. PubMed DOI PMC

Peacock C.S., Seeger K., Harris D., Murphy L., Ruiz J.C., Quail M.A., Peters N., Adlem E., Tivey A., Aslett M., et al. Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat. Genet. 2007;39:839–847. doi: 10.1038/ng2053. PubMed DOI PMC

Mesnil F., Brimont E. Sur un hématozoaire nouveau (Endotrypanum n. gen.) d’un édenté de la Guyane. C.R. Séances Soc. Biol. Ses. Fil. 1908;65:581–583.

Shaw J.J., Bird R.G. The endoerythrocytic habitat of a member of the Trypanosomatidae, Endotrypanum schaudinni, Mesnil and Brimont, 1908. Z. Trop. Parasitol. 1969;20:144–150. PubMed

Cunha A.M., Muniz J. Pesquisas sôbre o Endotrypanum schaudinni Mesnil e Brimont, 1908, parasita do Choloepus didactylus (L.) Mem. Do Inst. Oswaldo Cruz. 1944;41:179–193. doi: 10.1590/S0074-02761944000400010. DOI

Cupolillo E., Medina-Acosta E., Noyes H., Momen H., Grimaldi G., Jr. A revised classification for Leishmania and Endotrypanum. Parasitol. Today. 2000;16:142–144. doi: 10.1016/S0169-4758(99)01609-9. PubMed DOI

Shaw J.J. The Haemoflagellates of Sloths. H. K. Lewis; London, UK: 1969. p. 132.

Kreutzer R.D., Corredor A., Grimaldi G., Jr., Grogl M., Rowton E.D., Young D.G., Morales A., McMahon-Pratt D., Guzman H., Tesh R.B. Characterization of Leishmania colombiensis sp. n (Kinetoplastida: Trypanosomatidae), a new parasite infecting humans, animals, and phlebotomine sand flies in Colombia and Panama. Am. J. Trop. Med. Hyg. 1991;44:662–675. doi: 10.4269/ajtmh.1991.44.662. PubMed DOI

Zeledón R., Ponce C., Murillo J. Leishmania herreri sp. n. from sloths and sandflies of Costa Rica. J. Parasitol. 1979;65:275–279. doi: 10.2307/3280164. PubMed DOI

Delgado O., Castes M., White A.C., Jr., Kreutzer R.D. Leishmania colombiensis in Venezuela. Am. J. Trop. Med. Hyg. 1993;48:145–147. doi: 10.4269/ajtmh.1993.48.145. PubMed DOI

Rodriguez-Bonfante C., Bonfante-Garrido R., Grimaldi G., Jr., Momen H., Cupolillo E. Genotypically distinct Leishmania colombiensis isolates from Venezuela cause both cutaneous and visceral leishmaniasis in humans. Infect. Genet. Evol. J. Mol. Epidemiol. Evol. Genet. Infect. Dis. 2003;3:119–124. doi: 10.1016/S1567-1348(03)00012-1. PubMed DOI

Herrer A. Leishmania hertigi sp. n., from the tropical porcupine, Coendou rothschildi Thomas. J. Parasitol. 1971;57:626–629. doi: 10.2307/3277928. PubMed DOI

Lainson R., Shaw J.J. Leishmanias of neotropical porcupines: Leishmania hertigi deanei nov. subsp. Acta Amaz. 1977;7:51–57. doi: 10.1590/1809-43921977071051. DOI

Gardener P.J., Chance M.L., Peters W. Biochemical taxonomy of Leishmania. II: Electrophoretic variation of malate dehydrogenase. Ann. Trop. Med. Parasitol. 1974;68:317–325. doi: 10.1080/00034983.1974.11686954. PubMed DOI

da Silva D.A., Madeira Mde F., Barbosa Filho C.J., Schubach E.Y., Barros J.H., Figueiredo F.B. Leishmania (Leishmania) hertigi in a porcupine (Coendou sp.) found in Brasilia, Federal District, Brazil. Rev. Bras. Parasitol. Vet. 2013;22:297–299. doi: 10.1590/S1984-29612013005000014. PubMed DOI

Deane L.M., da Silva J.E., de Figueiredo P.Z. Leishmaniae in the viscera of porcupines from the state of Piaui, Brazil. Rev. Do Inst. De Med. Trop. De Sao Paulo. 1974;16:68–69. PubMed

Pothirat T., Tantiworawit A., Chaiwarith R., Jariyapan N., Wannasan A., Siriyasatien P., Supparatpinyo K., Bates M.D., Kwakye-Nuako G., Bates P.A. First isolation of Leishmania from Northern Thailand: Case report, identification as Leishmania martiniquensis and phylogenetic position within the Leishmania enriettii complex. PLoS Negl. Trop. Dis. 2014;8:e3339. doi: 10.1371/journal.pntd.0003339. PubMed DOI PMC

Shaw J.J. A possible vector of Endotrypanum schaudinni of the sloth Choloepus hoffmanni, in Panama. Nature. 1964;201:417–418. doi: 10.1038/201417a0. PubMed DOI

Shaw J.J., de Rosa A.T., Cruz A.C.R., Vasconcelos P.F.C. Brazilian phlebotomines as hosts and vectors of viruses, bacteria, fungi, protozoa (excluding those belonging to the genus Leishmania) and nematodes. In: Rangel E.F., Shaw J.J., editors. Brazilian Sand Flies. Springer International Publishing AG; Basel, Switzerland: 2018. pp. 417–441.

Shaw J.J. The behaviour of Endotrypanum schaudinni (Kinetoplastidae:Trypanosomatidae) in three species of laboratory-bred neotropical sandflies (Diptera:Psychodidae) and its influence on the classification of the genus Leishmania. In: Canning E.U., editor. Parasitological Topics. A Presentation Volume to P. C. C. Garnham, F. R. S., on the Occasion of His 80th Birthday. Allen Press; Lawrence, KS, USA: 1981. pp. 232–241.

Franco A.M., Tesh R.B., Guzman H., Deane M.P., Grimaldi Junior G. Development of Endotrypanum (Kinetoplastida:Trypanosomatidae) in experimentally infected phlebotomine sand flies (Diptera:Psychodidae) J. Med. Entomol. 1997;34:189–192. doi: 10.1093/jmedent/34.2.189. PubMed DOI

Katakura K., Mimori T., Furuya M., Uezato H., Nonaka S., Okamoto M., Gomez L.E., Hashiguchi Y. Identification of Endotrypanum species from a sloth, a squirrel and Lutzomyia sandflies in Ecuador by PCR amplification and sequencing of the mini-exon gene. J. Vet. Med. Sci. 2003;65:649–653. doi: 10.1292/jvms.65.649. PubMed DOI

Christensen H.A., Herrer A. Neotropical sand flies (Diptera: Psychodidae), invertebrate hosts of Endotrypanum schaudinni (Kinetoplastida: Trypanosomatidae) J. Med. Entomol. 1976;13:299–303. doi: 10.1093/jmedent/13.3.299. PubMed DOI

Thies S.F., Bronzoni R.V.M., Michalsky E.M., Santos E.S.D., Silva D., Dias E.S., Damazo A.S. Aspects on the ecology of phlebotomine sand flies and natural infection by Leishmania hertigi in the Southeastern Amazon Basin of Brazil. Acta Trop. 2018;177:37–43. doi: 10.1016/j.actatropica.2017.09.023. PubMed DOI

Barratt J., Kaufer A., Peters B., Craig D., Lawrence A., Roberts T., Lee R., McAuliffe G., Stark D., Ellis J. Isolation of novel trypanosomatid, Zelonia australiensis sp. nov. (Kinetoplastida: Trypanosomatidae) provides support for a Gondwanan origin of dixenous parasitism in the Leishmaniinae. PLoS Negl. Trop. Dis. 2017;11:e0005215. doi: 10.1371/journal.pntd.0005215. PubMed DOI PMC

Harkins K.M., Schwartz R.S., Cartwright R.A., Stone A.C. Phylogenomic reconstruction supports supercontinent origins for Leishmania. Infect. Genet. Evol. J. Mol. Epidemiol. Evol. Genet. Infect. Dis. 2016;38:101–109. doi: 10.1016/j.meegid.2015.11.030. PubMed DOI

O’Leary M.A., Bloch J.I., Flynn J.J., Gaudin T.J., Giallombardo A., Giannini N.P., Goldberg S.L., Kraatz B.P., Luo Z.X., Meng J., et al. The placental mammal ancestor and the post-K-Pg radiation of placentals. Science. 2013;339:662–667. doi: 10.1126/science.1229237. PubMed DOI

Lopes A.H., Iovannisci D., Petrillo-Peixoto M., McMahon-Pratt D., Beverley S.M. Evolution of nuclear DNA and the occurrence of sequences related to new small chromosomal DNAs in the trypanosomatid genus Endotrypanum. Mol. Biochem. Parasitol. 1990;40:151–161. doi: 10.1016/0166-6851(90)90037-M. PubMed DOI

Maslov D.A., Lukeš J., Jirků M., Simpson L. Phylogeny of trypanosomes as inferred from the small and large subunit rRNAs: Implications for the evolution of parasitism in the trypanosomatid protozoa. Mol. Biochem. Parasitol. 1996;75:197–205. doi: 10.1016/0166-6851(95)02526-X. PubMed DOI

Maslov D.A., Yurchenko V.Y., Jirků M., Lukeš J. Two new species of trypanosomatid parasites isolated from Heteroptera in Costa Rica. J. Eukaryot. Microbiol. 2010;57:177–188. doi: 10.1111/j.1550-7408.2009.00464.x. PubMed DOI

Yurchenko V., Votýpka J., Tesařová M., Klepetková H., Kraeva N., Jirků M., Lukeš J. Ultrastructure and molecular phylogeny of four new species of monoxenous trypanosomatids from flies (Diptera: Brachycera) with redefinition of the genus Wallaceina. Folia Parasitol. 2014;61:97–112. doi: 10.14411/fp.2014.023. PubMed DOI

Losev A., Grybchuk-Ieremenko A., Kostygov A.Y., Lukes J., Yurchenko V. Host specificity, pathogenicity, and mixed infections of trypanoplasms from freshwater fishes. Parasitol. Res. 2015;114:1071–1078. doi: 10.1007/s00436-014-4277-y. PubMed DOI

Kostygov A.Y., Grybchuk-Ieremenko A., Malysheva M.N., Frolov A.O., Yurchenko V. Molecular revision of the genus Wallaceina. Protist. 2014;165:594–604. doi: 10.1016/j.protis.2014.07.001. PubMed DOI

Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990;215:403–410. doi: 10.1016/S0022-2836(05)80360-2. PubMed DOI

Bolger A.M., Lohse M., Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. PubMed DOI PMC

Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data. [(accessed on 8 March 2021)]; Available online: http://www.bioinformatics.babraham.ac.uk/projects/fastqc.

Bankevich A., Nurk S., Antipov D., Gurevich A.A., Dvorkin M., Kulikov A.S., Lesin V.M., Nikolenko S.I., Pham S., Prjibelski A.D., et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. J. Comput. Mol. Cell Biol. 2012;19:455–477. doi: 10.1089/cmb.2012.0021. PubMed DOI PMC

Laetsch D.R., Blaxter M.L. BlobTools: Interrogation of genome assemblies. F1000Research. 2017;6:1287. doi: 10.12688/f1000research.12232.1. DOI

Mikheenko A., Prjibelski A., Saveliev V., Antipov D., Gurevich A. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics. 2018;34:i142–i150. doi: 10.1093/bioinformatics/bty266. PubMed DOI PMC

Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 2012;9:357–359. doi: 10.1038/nmeth.1923. PubMed DOI PMC

Kim D., Paggi J.M., Park C., Bennett C., Salzberg S.L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 2019;37:907–915. doi: 10.1038/s41587-019-0201-4. PubMed DOI PMC

Steinbiss S., Silva-Franco F., Brunk B., Foth B., Hertz-Fowler C., Berriman M., Otto T.D. Companion: A web server for annotation and analysis of parasite genomes. Nucleic Acids Res. 2016;44:W29–W34. doi: 10.1093/nar/gkw292. PubMed DOI PMC

Waterhouse R.M., Seppey M., Simão F.A., Manni M., Ioannidis P., Klioutchnikov G., Kriventseva E.V., Zdobnov E.M. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol. Biol. Evol. 2018;35:543–548. doi: 10.1093/molbev/msx319. PubMed DOI PMC

Smit A.F.A., Hubley R., Green P. RepeatMasker Open-4.0. [(accessed on 19 March 2021)]; Available online: http://www.repeatmasker.org.

Soderlund C., Nelson W., Shoemaker A., Paterson A. SyMAP: A system for discovering and viewing syntenic regions of FPC maps. Genome Res. 2006;16:1159–1168. doi: 10.1101/gr.5396706. PubMed DOI PMC

Tamazian G., Dobrynin P., Krasheninnikova K., Komissarov A., Koepfli K.P., O’Brien S.J. Chromosomer: A reference-based genome arrangement tool for producing draft chromosome sequences. Gigascience. 2016;5:38. doi: 10.1186/s13742-016-0141-6. PubMed DOI PMC

Quinlan A.R. BEDTools: The swiss-army tool for genome feature analysis. Curr. Protoc. Bioinform. 2014;47:11–12. doi: 10.1002/0471250953.bi1112s47. PubMed DOI PMC

Wickham H., François R., Henry L., Müller K. Dplyr: A Grammar of Data Manipulation. R Package Version 1.0.2. 2020.

Ginestet C. ggplot2: Elegant graphics for data analysis. J. R. Stat. Soc. 2011;174:245. doi: 10.1111/j.1467-985X.2010.00676_9.x. DOI

Lipovetsky S. Statistical inference via data science: A modern dive into R and the tidyverse. Technometrics. 2020;62:283. doi: 10.1080/00401706.2020.1744908. DOI

Boyd Z., Hughes J. WeeSAM: Script for Parsing SAM/BAM Files for Coverage Statistics. 2018.

McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–1303. doi: 10.1101/gr.107524.110. PubMed DOI PMC

Rimmer A., Phan H., Mathieson I., Iqbal Z., Twigg S.R., Wilkie A.O., McVean G., Lunter G. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat. Genet. 2014;46:912–918. doi: 10.1038/ng.3036. PubMed DOI PMC

Emms D.M., Kelly S. OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20:238. doi: 10.1186/s13059-019-1832-y. PubMed DOI PMC

Katoh K., Standley D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013;30:772–780. doi: 10.1093/molbev/mst010. PubMed DOI PMC

Capella-Gutiérrez S., Silla-Martinez J.M., Gabaldon T. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–1973. doi: 10.1093/bioinformatics/btp348. PubMed DOI PMC

Eddy S.R. Accelerated profile HMM searches. PLoS Comput. Biol. 2011;7:e1002195. doi: 10.1371/journal.pcbi.1002195. PubMed DOI PMC

Nguyen L.T., Schmidt H.A., von Haeseler A., Minh B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015;32:268–274. doi: 10.1093/molbev/msu300. PubMed DOI PMC

Lartillot N., Rodrigue N., Stubbs D., Richer J. PhyloBayes MPI: Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 2013;62:611–615. doi: 10.1093/sysbio/syt022. PubMed DOI

Yu G.C., Smith D.K., Zhu H.C., Guan Y., Lam T.T.Y. ggtree: An R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 2017;8:28–36. doi: 10.1111/2041-210X.12628. DOI

Csűrös M. Count: Evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics. 2010;26:1910–1912. doi: 10.1093/bioinformatics/btq315. PubMed DOI

Kanehisa M., Sato Y., Morishima K. BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. J. Mol. Biol. 2016;428:726–731. doi: 10.1016/j.jmb.2015.11.006. PubMed DOI

Jones P., Binns D., Chang H.Y., Fraser M., Li W., McAnulla C., McWilliam H., Maslen J., Mitchell A., Nuka G., et al. InterProScan 5: Genome-scale protein function classification. Bioinformatics. 2014;30:1236–1240. doi: 10.1093/bioinformatics/btu031. PubMed DOI PMC

Lex A., Gehlenborg N., Strobelt H., Vuillemot R., Pfister H. UpSet: Visualization of Intersecting Sets. IEEE Trans. Vis. Comput. Graph. 2014;20:1983–1992. doi: 10.1109/TVCG.2014.2346248. PubMed DOI PMC

Opperdoes F.R., Butenko A., Flegontov P., Yurchenko V., Lukeš J. Comparative metabolism of free-living Bodo saltans and parasitic trypanosomatids. J. Eukaryot. Microbiol. 2016;63:657–678. doi: 10.1111/jeu.12315. PubMed DOI

Binns D., Dimmer E., Huntley R., Barrell D., O’Donovan C., Apweiler R. QuickGO: A web-based tool for Gene Ontology searching. Bioinformatics. 2009;25:3045–3046. doi: 10.1093/bioinformatics/btp536. PubMed DOI PMC

Finn R.D., Coggill P., Eberhardt R.Y., Eddy S.R., Mistry J., Mitchell A.L., Potter S.C., Punta M., Qureshi M., Sangrador-Vegas A., et al. The Pfam protein families database: Towards a more sustainable future. Nucleic Acids Res. 2016;44:D279–D285. doi: 10.1093/nar/gkv1344. PubMed DOI PMC

Sievers F., Wilm A., Dineen D., Gibson T.J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., Soding J., et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011;7:539. doi: 10.1038/msb.2011.75. PubMed DOI PMC

Rambaut A. FigTree v.1.4.4. [(accessed on 19 March 2021)]; Available online: http://tree.bio.ed.ac.uk/software/figtree/

Krogh A., Larsson B., von Heijne G., Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 2001;305:567–580. doi: 10.1006/jmbi.2000.4315. PubMed DOI

Gerlt J.A., Bouvier J.T., Davidson D.B., Imker H.J., Sadkhin B., Slater D.R., Whalen K.L. Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. Biochim. Biophys. Acta. 2015;1854:1019–1037. doi: 10.1016/j.bbapap.2015.04.015. PubMed DOI PMC

Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–2504. doi: 10.1101/gr.1239303. PubMed DOI PMC

Butenko A., Hammond M., Field M.C., Ginger M.L., Yurchenko V., Lukeš J. Reductionist pathways for parasitism in euglenozoans? Expanded datasets provide new insights. Trends Parasitol. 2021;37:100–116. doi: 10.1016/j.pt.2020.10.001. PubMed DOI

Jackson A.P. The evolution of amastin surface glycoproteins in trypanosomatid parasites. Mol. Biol. Evol. 2010;27:33–45. doi: 10.1093/molbev/msp214. PubMed DOI PMC

Zhang J., Nielsen R., Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 2005;22:2472–2479. doi: 10.1093/molbev/msi237. PubMed DOI

Huerta-Cepas J., Serra F., Bork P. ETE 3: Reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 2016;33:1635–1638. doi: 10.1093/molbev/msw046. PubMed DOI PMC

Alexa A., Rahnenfuhrer J., Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006;22:1600–1607. doi: 10.1093/bioinformatics/btl140. PubMed DOI

Flegontov P., Butenko A., Firsov S., Kraeva N., Eliáš M., Field M.C., Filatov D., Flegontova O., Gerasimov E.S., Hlaváčová J., et al. Genome of Leptomonas pyrrhocoris: A high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania. Sci. Rep. 2016;6:23704. doi: 10.1038/srep23704. PubMed DOI PMC

Sloan M.A., Brooks K., Otto T.D., Sanders M.J., Cotton J.A., Ligoxygakis P. Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania. PLoS Genet. 2019;15:e1008452. doi: 10.1371/journal.pgen.1008452. PubMed DOI PMC

Szöör B. Trypanosomatid protein phosphatases. Mol. Biochem. Parasitol. 2010;173:53–63. doi: 10.1016/j.molbiopara.2010.05.017. PubMed DOI PMC

Soulat D., Bogdan C. Function of macrophage and parasite phosphatases in leishmaniasis. Front. Immunol. 2017;8:1838. doi: 10.3389/fimmu.2017.01838. PubMed DOI PMC

Orr G.A., Werner C., Xu J., Bennett M., Weiss L.M., Takvorkan P., Tanowitz H.B., Wittner M. Identification of novel serine/threonine protein phosphatases in Trypanosoma cruzi: A potential role in control of cytokinesis and morphology. Infect. Immun. 2000;68:1350–1358. doi: 10.1128/IAI.68.3.1350-1358.2000. PubMed DOI PMC

Kraeva N., Leštinová T., Ishemgulova A., Majerová K., Butenko A., Vaselek S., Bespyatykh J., Charyyeva A., Spitzová T., Kostygov A.Y., et al. LmxM.22.0250-encoded dual specificity protein/lipid phosphatase impairs Leishmania mexicana virulence in vitro. Pathogens. 2019;8:241. doi: 10.3390/pathogens8040241. PubMed DOI PMC

Qureshi R., Jakkula P., Sagurthi S.R., Qureshi I.A. Protein phosphatase 1 of Leishmania donovani exhibits conserved catalytic residues and pro-inflammatory response. Biochem. Biophys. Res. Commun. 2019;516:770–776. doi: 10.1016/j.bbrc.2019.06.085. PubMed DOI

Kaufer A., Stark D., Ellis J. Evolutionary insight into the Trypanosomatidae using alignment-free phylogenomics of the kinetoplast. Pathogens. 2019;8:157. doi: 10.3390/pathogens8030157. PubMed DOI PMC

Ludwig A., Krieger M.A. Genomic and phylogenetic evidence of VIPER retrotransposon domestication in trypanosomatids. Mem. Do Inst. Oswaldo Cruz. 2016;111:765–769. doi: 10.1590/0074-02760160224. PubMed DOI PMC

Kelly F.D., Sanchez M.A., Landfear S.M. Touching the surface: Diverse roles for the flagellar membrane in kinetoplastid parasites. Microbiol. Mol. Biol. Rev. Mmbr. 2020;84:e00079-19. doi: 10.1128/MMBR.00079-19. PubMed DOI PMC

Liu Q., Lei J., Darby A.C., Kadowaki T. Trypanosomatid parasite dynamically changes the transcriptome during infection and modifies honey bee physiology. Commun. Biol. 2020;3:51. doi: 10.1038/s42003-020-0775-x. PubMed DOI PMC

Rochette A., McNicoll F., Girard J., Breton M., Leblanc E., Bergeron M.G., Papadopoulou B. Characterization and developmental gene regulation of a large gene family encoding amastin surface proteins in Leishmania spp. Mol. Biochem. Parasitol. 2005;140:205–220. doi: 10.1016/j.molbiopara.2005.01.006. PubMed DOI

Myler P.J., Lodes M.J., Merlin G., de Vos T., Stuart K.D. An amplified DNA element in Leishmania encodes potential integral membrane and nucleotide-binding proteins. Mol. Biochem. Parasitol. 1994;66:11–20. doi: 10.1016/0166-6851(94)90031-0. PubMed DOI

Ravooru N., Paul O.S., Nagendra H.G., Sathyanarayanan N. Data enabled prediction analysis assigns folate/biopterin transporter (BT1) family to 36 hypothetical membrane proteins in Leishmania donovani. Bioinformation. 2019;15:697–708. doi: 10.6026/97320630015697. PubMed DOI PMC

Ouellette M., Drummelsmith J., El-Fadili A., Kundig C., Richard D., Roy G. Pterin transport and metabolism in Leishmania and related trypanosomatid parasites. Int. J. Parasitol. 2002;32:385–398. doi: 10.1016/S0020-7519(01)00346-0. PubMed DOI

Ouameur A.A., Girard I., Legare D., Ouellette M. Functional analysis and complex gene rearrangements of the folate/biopterin transporter (FBT) gene family in the protozoan parasite Leishmania. Mol. Biochem. Parasitol. 2008;162:155–164. doi: 10.1016/j.molbiopara.2008.08.007. PubMed DOI

Singer S.J. The structure and insertion of integral proteins in membranes. Annu. Rev. Cell Biol. 1990;6:247–296. doi: 10.1146/annurev.cb.06.110190.001335. PubMed DOI

El-Sayed N.M., Myler P.J., Blandin G., Berriman M., Crabtree J., Aggarwal G., Caler E., Renauld H., Worthey E.A., Hertz-Fowler C., et al. Comparative genomics of trypanosomatid parasitic protozoa. Science. 2005;309:404–409. doi: 10.1126/science.1112181. PubMed DOI

Opperdoes F.R., Coombs G.H. Metabolism of Leishmania: Proven and predicted. Trends Parasitol. 2007;23:149–158. doi: 10.1016/j.pt.2007.02.004. PubMed DOI

Opperdoes F., Michels P.A. The metabolic repertoire of Leishmania and implications for drug discovery. In: Myler P., Fasel N., editors. Leishmania: After the Genome. Caister Academic Press; Norfolk, UK: 2008. pp. 123–158.

Škodová-Sveráková I., Záhonová K., Bučková B., Füssy Z., Yurchenko V., Lukeš J. Catalase and ascorbate peroxidase in euglenozoan protists. Pathogens. 2020;9:317. doi: 10.3390/pathogens9040317. PubMed DOI PMC

Kraeva N., Horáková E., Kostygov A., Kořený L., Butenko A., Yurchenko V., Lukeš J. Catalase in Leishmaniinae: With me or against me? Infect. Genet. Evol. J. Mol. Epidemiol. Evol. Genet. Infect. Dis. 2017;50:121–127. doi: 10.1016/j.meegid.2016.06.054. PubMed DOI

Turnock D.C., Ferguson M.A. Sugar nucleotide pools of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major. Eukaryot. Cell. 2007;6:1450–1463. doi: 10.1128/EC.00175-07. PubMed DOI PMC

Boitz J.M., Yates P.A., Kline C., Gaur U., Wilson M.E., Ullman B., Roberts S.C. Leishmania donovani ornithine decarboxylase is indispensable for parasite survival in the mammalian host. Infect. Immun. 2009;77:756–763. doi: 10.1128/IAI.01236-08. PubMed DOI PMC

Moreira D.S., Xavier M.V., Murta S.M.F. Ascorbate peroxidase overexpression protects Leishmania braziliensis against trivalent antimony effects. Mem. Do Inst. Oswaldo Cruz. 2018;113:e180377. doi: 10.1590/0074-02760180377. PubMed DOI PMC

Sunter J.D., Yanase R., Wang Z., Catta-Preta C.M.C., Moreira-Leite F., Myšková J., Pružinová K., Volf P., Mottram J.C., Gull K. Leishmania flagellum attachment zone is critical for flagellar pocket shape, development in the sand fly, and pathogenicity in the host. Proc. Natl. Acad. Sci. USA. 2019;116:6351–6360. doi: 10.1073/pnas.1812462116. PubMed DOI PMC

Teixeira S.M., Russell D.G., Kirchhoff L.V., Donelson J.E. A differentially expressed gene family encoding “amastin”, a surface protein of Trypanosoma cruzi amastigotes. J. Biol. Chem. 1994;269:20509–20516. doi: 10.1016/S0021-9258(17)32022-7. PubMed DOI

Wu Y., El Fakhry Y., Sereno D., Tamar S., Papadopoulou B. A new developmentally regulated gene family in Leishmania amastigotes encoding a homolog of amastin surface proteins. Mol. Biochem. Parasitol. 2000;110:345–357. doi: 10.1016/S0166-6851(00)00290-5. PubMed DOI

Coughlin B.C., Teixeira S.M., Kirchhoff L.V., Donelson J.E. Amastin mRNA abundance in Trypanosoma cruzi is controlled by a 3′-untranslated region position-dependent cis-element and an untranslated region-binding protein. J. Biol. Chem. 2000;275:12051–12060. doi: 10.1074/jbc.275.16.12051. PubMed DOI

Stober C.B., Lange U.G., Roberts M.T., Alcami A., Blackwell J.M. IL-10 from regulatory T cells determines vaccine efficacy in murine Leishmania major infection. J. Immunol. 2005;175:2517–2524. doi: 10.4049/jimmunol.175.4.2517. PubMed DOI

Ribeiro P.A.F., Vale D.L., Dias D.S., Lage D.P., Mendonca D.V.C., Ramos F.F., Carvalho L.M., Carvalho A., Steiner B.T., Roque M.C., et al. Leishmania infantum amastin protein incorporated in distinct adjuvant systems induces protection against visceral leishmaniasis. Cytokine. 2020;129:155031. doi: 10.1016/j.cyto.2020.155031. PubMed DOI

Pérez-Díaz L., Silva T.C., Teixeira S.M. Involvement of an RNA binding protein containing Alba domain in the stage-specific regulation of beta-amastin expression in Trypanosoma cruzi. Mol. Biochem. Parasitol. 2017;211:1–8. doi: 10.1016/j.molbiopara.2016.12.005. PubMed DOI

Butenko A., Opperdoes F.R., Flegontova O., Horak A., Hampl V., Keeling P., Gawryluk R.M.R., Tikhonenkov D., Flegontov P., Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol. 2020;18:23. doi: 10.1186/s12915-020-0754-1. PubMed DOI PMC

Raymond F., Boisvert S., Roy G., Ritt J.F., Legare D., Isnard A., Stanke M., Olivier M., Tremblay M.J., Papadopoulou B., et al. Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species. Nucleic Acids Res. 2012;40:1131–1147. doi: 10.1093/nar/gkr834. PubMed DOI PMC

Wilson V., Southgate B. Lizard Leishmania. In: Lumsden W., Evans D.A., editors. Biology of Kinetoplastida. Academic Press; New York, NY, USA: 1979. pp. 242–268.

Ovezmukhammedov A., Saf’ianova V.M. Taxonomic problems of the Leishmania of reptiles. Parazitologiia. 1989;23:334–343. (In Russian) PubMed

de Paiva R.M., Grazielle-Silva V., Cardoso M.S., Nakagaki B.N., Mendonca-Neto R.P., Canavaci A.M., Souza Melo N., Martinelli P.M., Fernandes A.P., daRocha W.D., et al. Amastin knockdown in Leishmania braziliensis affects parasite-macrophage interaction and results in impaired viability of intracellular amastigotes. PLoS Pathog. 2015;11:e1005296. doi: 10.1371/journal.ppat.1005296. PubMed DOI PMC

de Menezes J.P., Saraiva E.M., da Rocha-Azevedo B. The site of the bite: Leishmania interaction with macrophages, neutrophils and the extracellular matrix in the dermis. Parasites Vectors. 2016;9:264. doi: 10.1186/s13071-016-1540-3. PubMed DOI PMC

Pinheiro L.J., Paranaiba L.F., Alves A.F., Parreiras P.M., Gontijo N.F., Soares R.P., Tafuri W.L. Salivary gland extract modulates the infection of two Leishmania enriettii strains by interfering with macrophage differentiation in the model of Cavia porcellus. Front. Microbiol. 2018;9:969. doi: 10.3389/fmicb.2018.00969. PubMed DOI PMC

Jain M., Dole V.S., Myler P.J., Stuart K.D., Madhubala R. Role of biopterin transporter (BT1) gene on growth and infectivity of Leishmania. Am. J. Biochem. Biotechnol. 2007;3:199–206. doi: 10.3844/ajbbsp.2007.199.206. DOI

A lineage-specific protein network at the trypanosome nuclear envelope

In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code

Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae

Kinetoplast Genome of Leishmania spp. Is under Strong Purifying Selection

Comparative Analysis of Three Trypanosomatid Catalases of Different Origin

Genomics of Trypanosomatidae: Where We Stand and What Needs to Be Done?