Title : Genomic analysis of zhoor genome sequencing of leishmania major
Abstract:
Leishmaniases represent a major public health problem not only because of the number of cases recorded each year, but also because of the wide distribution of the disease. It is a parasitic disease caused by around 20 species of flagellated protozoa transmitted by the bite of certain species of sandfly, causing a spectrum of clinical pathology in humans ranging from disfiguring skin lesions to fatal visceral Leishmaniases. Cutaneous leishmaniasis due to Leishmania major is a polymorphic disease; in fact the infection can be asymptomatic, localized, or disseminated. This clinical polymorphism may reflect the variability of the host's immune response and / or the genetic diversity of the parasite. The objective of this work is to determine the genomic diversity that contributes to clinical variability, by trying to identify the variation in chromosome number and to extract SNPs and InDels.
The genomic study is based on four sequences (whole genome) of Leishmania major available on National Center of Biotechnology Information in Fastq form, from three countries: Tunisia, Algeria and Israel, analysis of NGS data is set up from a pipeline to facilitate the discovery of genetic diversity, in particular single-nucleotide polymorphisms and chromosomal somy. The results obtained from SNP annotation suggest variability in the number of InDels and Insertions even between strains from the same country and analysis of median chromosomal depth shows a dominant chromosome form of trisome for the four strains of L. major and a tetrasomy form for chromosome 29 of the strain from Israel.
Key words : Leishmania major, cutaneous Leishmania, NGS, bio-informatique, Somy , Variant calling
