title: Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania.
abstract: Many high-quality genomes are available for dixenous (two hosts) trypanosomatid species of the genera Trypanosoma, Leishmania, and Phytomonas, but only fragmentary information is available for monoxenous (single-host) trypanosomatids. In trypanosomatids, monoxeny is ancestral to dixeny, thus it is anticipated that the genome sequences of the key monoxenous parasites will be instrumental for both understanding the origin of parasitism and the evolution of dixeny. Here, we present a high-quality genome for Leptomonas pyrrhocoris, which is closely related to the dixenous genus Leishmania. The L. pyrrhocoris genome (30.4 Mbp in 60 scaffolds) encodes 10,148 genes. Using the L. pyrrhocoris genome, we pinpointed genes gained in Leishmania. Among those genes, 20 genes with unknown function had expression patterns in the Leishmania mexicana life cycle suggesting their involvement in virulence. By combining differential expression data for L. mexicana, L. major and Leptomonas seymouri, we have identified several additional proteins potentially involved in virulence, including SpoU methylase and U3 small nucleolar ribonucleoprotein IMP3. The population genetics of L. pyrrhocoris was also addressed by sequencing thirteen strains of different geographic origin, allowing the identification of 1,318 genes under positive selection. This set of genes was significantly enriched in components of the cytoskeleton and the flagellum.
authors.affiliation: Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.|Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.|Institute for Information Transmission Problems, Russian Academy of Sciences, 127051, Moscow, Russia.
authors.forename: Pavel
authors.initials: P
authors.lastname: Flegontov
authors.affiliation: Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
authors.forename: Anzhelika
authors.initials: A
authors.lastname: Butenko
authors.affiliation: Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.
authors.forename: Sergei
authors.initials: S
authors.lastname: Firsov
authors.affiliation: Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
authors.forename: Natalya
authors.initials: N
authors.lastname: Kraeva
authors.affiliation: Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.|Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
authors.forename: Marek
authors.initials: M
authors.lastname: Eliáš
authors.affiliation: School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
authors.forename: Mark C
authors.initials: MC
authors.lastname: Field
authors.affiliation: Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Filatov
authors.affiliation: Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.
authors.forename: Olga
authors.initials: O
authors.lastname: Flegontova
authors.affiliation: Institute for Information Transmission Problems, Russian Academy of Sciences, 127051, Moscow, Russia.|Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia.|Department of Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia.
authors.forename: Evgeny S
authors.initials: ES
authors.lastname: Gerasimov
authors.affiliation: Department of Parasitology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic.
authors.forename: Jana
authors.initials: J
authors.lastname: Hlaváčová
authors.affiliation: Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
authors.forename: Aygul
authors.initials: A
authors.lastname: Ishemgulova
authors.affiliation: Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L3 5RF, UK.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Jackson
authors.affiliation: Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
authors.forename: Steve
authors.initials: S
authors.lastname: Kelly
authors.affiliation: Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
authors.forename: Alexei Y
authors.initials: AY
authors.lastname: Kostygov
authors.affiliation: Institute for Information Transmission Problems, Russian Academy of Sciences, 127051, Moscow, Russia.|Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Logacheva
authors.affiliation: Department of Biology; University of California at Riverside, Riverside, 92521, CA USA.
authors.forename: Dmitri A
authors.initials: DA
authors.lastname: Maslov
authors.affiliation: de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium.
authors.forename: Fred R
authors.initials: FR
authors.lastname: Opperdoes
authors.affiliation: School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
authors.forename: Amanda
authors.initials: A
authors.lastname: O'Reilly
authors.affiliation: Department of Parasitology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic.
authors.forename: Jovana
authors.initials: J
authors.lastname: Sádlová
authors.affiliation: Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.|Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
authors.forename: Tereza
authors.initials: T
authors.lastname: Ševčíková
authors.affiliation: School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
authors.forename: Divya
authors.initials: D
authors.lastname: Venkatesh
authors.affiliation: Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic.
authors.forename: Čestmír
authors.initials: Č
authors.lastname: Vlček
authors.affiliation: Department of Parasitology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Volf
authors.affiliation: Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.|Department of Parasitology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Votýpka
authors.affiliation: Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.|Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
authors.forename: Kristína
authors.initials: K
authors.lastname: Záhonová
authors.affiliation: Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.|Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.|Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
authors.forename: Vyacheslav
authors.initials: V
authors.lastname: Yurchenko
authors.affiliation: Biology Centre, Institute of Parasitology, 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.|Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada.
authors.forename: Julius
authors.initials: J
authors.lastname: Lukeš
mesh_terms: D004734:Energy Metabolism / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods; D063990:Gene Ontology; D017125:Genes, Protozoan / Q000235:genetics; D018503:Genome, Protozoan / Q000235:genetics*; D007891:Leishmania / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D010802:Phylogeny; D013045:Species Specificity; D014351:Trypanosomatina / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D014774:Virulence / Q000235:genetics