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.

Belozersky Institute of Physico Chemical Biology M 5 Lomonosov Moscow State University 119991 Moscow Russia

Biology Centre Institute of Parasitology Czech Academy of Sciences 370 05 České Budějovice Czech Republic

Canadian Institute for Advanced Research Toronto ON M5G 1Z8 Canada

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

Department of Biology; University of California at Riverside Riverside 92521 CA USA

Department of Infection Biology Institute of Infection and Global Health University of Liverpool Liverpool L3 5RF UK

Department of Parasitology Faculty of Science Charles University 128 44 Prague Czech Republic

Department of Plant Sciences University of Oxford Oxford OX1 3RB UK

e Duve Institute Université Catholique de Louvain 1200 Brussels Belgium

Faculty of Science University of South Bohemia 370 05 České Budějovice Czech Republic

Institute for Information Transmission Problems Russian Academy of Sciences 127051 Moscow Russia

Institute of Environmental Technologies Faculty of Science University of Ostrava 710 00 Ostrava Czech Republic

Institute of Molecular Genetics Czech Academy of Sciences 142 20 Prague Czech Republic

Life Science Research Centre Faculty of Science University of Ostrava 710 00 Ostrava Czech Republic

School of Life Sciences University of Dundee Dundee DD1 5EH UK

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