Genetic diversity and comparative genomics across Leishmania (Viannia) species

Abstract

Leishmaniasis is an important public health problem worldwide, with a broad spectrum of clinical and epidemiological features partly associated with the diversity and complex life cycle of the Leishmania parasites. This study analyzes genomic data from 205 Leishmania (Viannia) samples, including 65 newly sequenced clinical isolates. It also provides chromosome-level genome assemblies for 10 isolates representing different species and populations. The observed distribution of Leishmania genomic diversity across the sampling locations suggests rapid adaptation to different ecosystems. The phylogenomic analysis provides new hypotheses challenging the current delimitation of species. Pangenomic analysis of high-quality assemblies shows consistent copy number variation between species for different gene families. Larger and more diverse amastin gene families were observed in the assembled genomes compared to previous reports based on the analysis of short-read data. This work provides genomic resources and helpful information regarding central problems in the biology of Leishmania spp, including species diversification, transmission dynamics, and the evolution of virulence mechanisms.

Fig. 1. Maximum Likelihood phylogenetic reconstruction of Leishmania (Viannia) isolates.

The tree was built from 673,944 SNPs segregating within L. (Viannia) after filtering to keep genotype calls with quality >40, biallelic sites, MAF > 0.01, and 200 genotyped individuals. Chromosome 31, missense, and nonsense variants were removed. The tree was rooted at the midpoint. Branch support was calculated with a 1000 ultrafast bootstrap on IQtree. Isolates are colored according to the species. A detailed visualization of branches for isolates within species can be seen in the visualization of the tree available at the Supplementary Fig. S4.

Fig. 2. Genetic diversity of Leishmania (Viannia) species.

A Admixture analysis for L. (V.) braziliensis and L. (V.) peruviana. B Distance tree based on the L. (V.) braziliensis and L. (V.) peruviana SNPs identified in comparison to the M2904 L. (V.) braziliensis strain. Labels show the Pi diversity statistic. C Admixture analysis for L. (V.) guyanensis and L. (V.) panamensis. D Distance tree based on the L. (V.) guyanensis and L. (V.) panamensis SNPs identified in comparison to the M2904 L. (V.) braziliensis strain. Labels show the Pi diversity statistic. Subpopulation names are assigned for the larger species: L. (V.) braziliensis is composed of Lbra1 (Brazilian samples), Lbra2 (Colombian samples from the Andean region), Lbra3 (Colombian samples from the Orinoco-Amazonian region), Lbra4 (Peruvian samples); L. (V.) guyanensis is composed of Lguy1 (Colombian samples from the Andean region (4 samples), and 4 samples from Venezuela, French Guyana and Brazil) and Lguy2 (Colombian samples from the Pacific region); L. (V.) panamensis is composed of Lpan1 (Panamanian samples), Lpan2 (Colombian samples from the Pacific-Andean region), Lpan3 (Colombian samples from the Andean-Caribbean region), Lpan4 (Colombian samples from the Andean-Amazonian region); L. (V.) peruviana is composed of Lper1 (Peruvian samples from Porculla region) and Lper2 (Peruvian samples from the Surco region).

Fig. 3. Genomic structure and main characteristics of Leishmania (Viannia) genomes.

A–C Circos plots with main genomic features for A the LL0249 L. (V.) braziliensis isolate, B the UN0003 L. (V.) guyanensis isolate, and C the LL0536 L. (V.) panamensis isolate. The tracks show (i) GC content, (ii) density of core-genes, (iii) the density of genes coding for amastin surface glycoproteins, (iv) distribution of multi-copy gene families (at least 5 copies), (v) strand switches, (vi) distribution of TATE retroposons, (vii) Illumina sequencing depth (0–300×), (viii) Nanopore sequencing depth (0–100×). D Genome alignment of the M2904 and PSC-1 reference genomes and the assembled genomes of the isolates LL0249, UN0003, and LL0536.

Fig. 4. Amastin surface glycoproteins evolution within Leishmania (Viannia) isolates.

A Amastins maximum-likelihood phylogeny using the entire repertoire of amastins in 10 Leishmania (Viannia) genomes. Branches colors show the bootstrap values. The color of the nodes corresponds to the species complex, and the color of the outer strip corresponds to the chromosome where each sequence was found. Chr30 corresponds to β-amastins, Chr28 and 14 correspond to α-amastins, Chr24 corresponds to γ-amastins. The remaining chromosomes correspond to δ-amastins. B Conserved domains between amastin proteins represented as the MEME logo for each domain. C Pattern of conserved domains in each amastin subfamily. D, E Ks and Ka/Ks respectively among close and distant amastin paralogs of Leishmania (Viannia) isolates: LL0249 and UN0036 (L. (V.) braziliensis), UN0003 (L. (V.) guyanensis), LL0536 (L. (V.) panamensis). See sample sizes and p values in the Supplementary Table S5. F, G Ks and Ka/Ks respectively among amastin orthologs of Leishmania (Viannia) isolates: LL0249 (L. (V.) braziliensis), UN0003 (L. (V.) guyanensis), LL0536 (L. (V.) panamensis). See sample sizes and p values in the Supplementary Table S6. Middle lines are medians and box limits represent first (Q1) and third (Q3) quartiles. Lines are drawn from Q1 minus 1.5 of the interquartile range (IQR) to Q3 + 1.5*IQR.