Genomic Confirmation of Hybridisation and Recent Inbreeding in a Vector-Isolated Leishmania Population

Abstract

Although asexual reproduction via clonal propagation has been proposed as the principal reproductive mechanism across parasitic protozoa of the Leishmania genus, sexual recombination has long been suspected, based on hybrid marker profiles detected in field isolates from different geographical locations. The recent experimental demonstration of a sexual cycle in Leishmania within sand flies has confirmed the occurrence of hybridisation, but knowledge of the parasite life cycle in the wild still remains limited. Here, we use whole genome sequencing to investigate the frequency of sexual reproduction in Leishmania, by sequencing the genomes of 11 Leishmania infantum isolates from sand flies and 1 patient isolate in a focus of cutaneous leishmaniasis in the Çukurova province of southeast Turkey. This is the first genome-wide examination of a vector-isolated population of Leishmania parasites. A genome-wide pattern of patchy heterozygosity and SNP density was observed both within individual strains and across the whole group. Comparisons with other Leishmania donovani complex genome sequences suggest that these isolates are derived from a single cross of two diverse strains with subsequent recombination within the population. This interpretation is supported by a statistical model of the genomic variability for each strain compared to the L. infantum reference genome strain as well as genome-wide scans for recombination within the population. Further analysis of these heterozygous blocks indicates that the two parents were phylogenetically distinct. Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred. This observation allowed us to estimate the relative rates of sexual and asexual reproduction within this population, to our knowledge the first quantitative estimate of these events during the Leishmania life cycle.

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

“…Near-clading agreement between Internal Transcribed Spacer, MLEE, MLST, miniexon typing and gp63 intergenic RFLP has also been observed (Mauricio et al, 2006). In Turkey, a monophyletic near-clade has been delimitated by WGS and PCR-MLST, with concordance with MLEE (Rogers et al, 2014). In Latin America, near-clading agreement is obtained between: (1) STRUCTURE and NJ and (2) MLEE and microsatellites .…”

“…On the contrary, it is a fine illustration of it. As a matter of fact, within this near-clade, reproduction is 'primarily clonal'; 'intraspecific linkage patterns show low levels of recent recombination', which 'may have been an infrequent event'; and one observes 'mainly clonal reproduction in the parasite population', according to the very terms of the authors (Rogers et al, 2014).…”

“…The results are especially convincing for Leishmania (Boité et al, 2012;Downing et al, 2011;Inbar et al, 2013;Lachaud et al, 2014;Mannaert et al, 2012;Rogers et al, 2011Rogers et al, , 2014Sterkers et al, 2011Sterkers et al, , 2012Sterkers et al, , 2014, but are also available for T. cruzi (Buscaglia et al, 2015;Minning et al, 2011;Reis-Cunha et al, 2015;Souza et al, 2011). Aneuploidy is also frequent in C. albicans and C. neoformans (Ene and Bennet, 2014;McManus and Coleman, 2014;Ni et al, 2013).…”

“…e Rajendran et al (2012) b,e Ramírez et al (2012) e Razakandrainibe et al (2005) b,c Rezende et al (2010) e Rogers et al (2014) a,e Rougeron et al (2009Rougeron et al ( , 2010Rougeron et al ( , 2014Rougeron et al ( , 2015 ) Sibley and Ajioka (2008) b,c…”

“…High microsatellite diversity within this group of parasites, which appeared monomorphic with MLEE, illustrates the fact that 'identical genotypes' is a relative notion, that depends highly on the resolution power and mutation rate of the concerned marker (see 'Identical Multilocus Genotypes is a Relative Notion'). The use of powerful markers (WGS and PCR-MLST) has made it possible to discriminate a monophyletic group (near-clade) in Turkish L. infantum strains (Rogers et al, 2014). This near-clade corresponds to a unique MLEE MLG, again another case where a powerful marker (PCR-MLST) reveals additional genetic variability within a given MLG.…”