Genomic Diversification, Structural Plasticity, and Hybridization in Leishmania (Viannia) braziliensis

Abstract

Leishmania (Viannia) braziliensis is an important Leishmania species circulating in several Central and South American countries. Among Leishmania species circulating in Brazil, Argentina and Colombia, L. braziliensis has the highest genomic variability. However, genomic variability at the whole genome level has been only studied in Brazilian and Peruvian isolates; to date, no Colombian isolates have been studied. Considering that in Colombia, L. braziliensis is a species with great clinical and therapeutic relevance, as well as the role of genetic variability in the epidemiology of leishmaniasis, we analyzed and evaluated intraspecific genomic variability of L. braziliensis from Colombian and Bolivian isolates and compared them with Brazilian isolates. Twenty-one genomes were analyzed, six from Colombian patients, one from a Bolivian patient, and 14 Brazilian isolates downloaded from public databases. The results obtained of Phylogenomic analysis showed the existence of four well-supported clades, which evidenced intraspecific variability. The whole-genome analysis revealed structural variations in the somy, mainly in the Brazilian genomes (clade 1 and clade 3), low copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs) in all genomes analyzed. Interestingly, the genomes belonging to clades 2 and 3 from Colombia and Brazil, respectively, were characterized by low heterozygosity (~90% of SNP loci were homozygous) and regions suggestive of loss of heterozygosity (LOH). Additionally, we observed the drastic whole genome loss of heterozygosity and possible hybridization events in one genome belonging to clade 4. Unique/shared SNPs between and within the four clades were identified, revealing the importance of some of them in biological processes of L. braziliensis. Our analyses demonstrate high genomic variability of L. braziliensis in different regions of South America, mainly in Colombia and suggest that this species exhibits striking genomic diversity and a capacity of genomic hybridization; additionally, this is the first study to report whole-genome sequences of Colombian L. braziliensis isolates.

Variation inLeishmaniachemokine suppression driven by diversification of the GP63 virulence factor

“…(V.) panamensis and 7 L. (V.) braziliensis parasites. Raw data (.sra) were downloaded from two previous studies (44,45). The module fastq-dump from NCBI SRA toolkit v2.10.9…”

“…We next sought to determine the potential for the relative amounts of D463 and N463 alleles to contribute to variation in leishmaniasis by analyzing GP63 sequence variation from recently isolated parasites from Colombia and Bolivia (44,45). Patino et al sequenced whole genomes from parasites (19 L. (V.) panamensis(44) and 7 L. (V.) braziliensis( 45)) from 26 infected patients.…”

“…To quantify the natural diversity of GP63 sites involved in CXCL10 substrate specificity, we reassembled the whole genomes of 26 samples from Viannia subgenus parasites, including 19 L. (V.) panamensis and 7 L. (V.) braziliensis parasites. Raw data (.sra) were downloaded from two previous studies (44,45). The module fastq-dump from NCBI SRA toolkit v2.10.9…”

“…suppression. Specific changes that have been selected for in L. panamensis and other Viannia parasites markedly reduce CXCL10 cleavage while having minimal effect on overall proteolytic activity.Within the Viannia subgenus, clinical isolates of L. (V.) braziliensis have a higher proportion of the CXCL10 cleaving GP63 D463 allele compared to L. (V.) panamensis.We next sought to determine the potential for the relative amounts of D463 and N463 alleles to contribute to variation in leishmaniasis by analyzing GP63 sequence variation from recently isolated parasites from Colombia and Bolivia(44,45).Patino et al sequenced whole genomes from parasites (19 L. (V.) panamensis(44) and 7 L. (V.) braziliensis(45)) from 26 infected patients. Due to the high rates of gp63 gene duplication and copy number variation, significant genetic heterogeneity occurs among parasite isolates and structure of the region is poorly understood even in the reference PSC-1 strain.…”

Distinct Microbial Communities Colonize Tonsillar Squamous Cell Carcinoma

“…Finally, taxonomy was assigned based on the RDP trainset 16/release 11.5 [49] and the HOMD v.15.1 [24] database by applying the ‚assignTaxonomy' function from the dada2 package that utilizes the RDP Naive Bayesian Classi er described by Wang et al [50], with kmer size = 8, and 100 bootstrap replicates. In order to further infer phylogenetic relationships R/bioconductor packages msa v.1.18.0 [51] and phangorn v.2.5.5 [52] were used to build multiple sequence alignments and construct a phylogenetic tree. Before downstream analysis samples were rare ed to an even sampling depth of 500 reads using the R/bioconductor package phyloseq v.1.32.0 [53].…”