Leishmania, a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in a small subset of chromosomes using fluorescence hybridization methods. This phenomenon, termed mosaic aneuploidy (MA) might have important evolutionary and functional implications, but remains under-explored due to technological limitations. Here, we applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype heterogeneity in two Leishmania clonal populations representing different stages of MA evolution in vitro. We found that drastic changes in karyotypes quickly emerge in a population stemming from an almost euploid founder cell. This possibly involves polyploidization/hybridization at an early stage of population expansion, followed by assorted ploidy reduction. During further stages of expansion, MA increases by moderate and gradual karyotypic alterations. MA usually affected a defined subset of chromosomes, of which some display enrichment in snoRNA genes which could represent an adaptative benefit to the amplification of these chromosomes. Our data provide the first complete characterization of MA in Leishmania and pave the way for further functional studies.

14Maintenance of stable ploidy over continuous mitotic events is a paradigm for most higher 15 eukaryotes. Defects in chromosome segregation and/or replication can lead to aneuploidy, a 16 condition often considered deleterious. However, in Leishmania, a Protozoan parasite, 17aneuploidy is a constitutive feature, where variations of somies represent a mechanism of gene 18 expression adaptation, possibly impacting phenotypes. Strikingly, clonal Leishmania 19 populations display cell-to-cell somy variation, a phenomenon named mosaic aneuploidy (MA). 20However, until recently, no method was available for the determination of the complete 21 karyotype of single Leishmania parasites. To overcome this limitation, we used here for the first 22 time a high-throughput single-cell genomic sequencing (SCGS) method to estimate individual 23 karyotypes of 1560 promastigote cells in a clonal population of Leishmania donovani. We 24 identified 128 different karyotypes, of which 4 were dominant. A network analysis revealed that 25 most karyotypes are linked to each other by changes in copy number of a single chromosome 26 and allowed us to propose a hypothesis of MA evolution. Moreover, aneuploidy patterns that 27 were previously described by Bulk Genome Sequencing as emerging during first contact of 28 promastigotes populations with different drugs are already pre-existing in single karyotypes in 29 the SCGS data, suggesting a (pre-)adaptive role of MA. Additionally, the degree of somy 30 variation was chromosome-specific. The SCGS also revealed a small fraction of cells where one 31 or more chromosomes were nullisomic. Together, these results demonstrate the power of SCGS 32to resolve sub-clonal karyotype heterogeneity in Leishmania and pave the way for 33understanding the role of MA in these parasites' adaptability. 34 35