Genome mutations of the Turkish strain Leishmania infantum_TR01

• Published in: Infection, genetics and evolution Vol. 92; p. 104907
• Main Authors: Guldemir, Dilek, Nalbantoglu, Ayse Serpil
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.08.2021
• Subjects: Genome, Protozoan; Leishmania infantum - genetics; Leishmania infantum_TR01; Mutation; Next-generation sequencing technology; Polymorphism, Genetic; Protein-coding-polymorphisms; Turkey; Whole Genome Sequencing; Turkey; Next-generation sequencing technology; Protein-coding-polymorphisms; Leishmania infantum_TR01; Whole-genome sequencing
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2021.104907

Today, almost 15 years have passed since the whole genome sequence (WGS) of a Leishmania parasite was completed for the first time. However, information on the genetics of these parasites remains to be elucidated. Genome-based studies may contribute to control strategies for leishmaniasis. The increase in genetically based studies, particularly whole-genome sequencing studies on Leishmania, will contribute to the control of leishmaniasis, which is a common and neglected disease worldwide. Our previous study obtained the Leishmania infantum_TR01 (Lin_TR01) genome sequence (Guldemir et al., 2020). In the present study, we focused on the mutations detected in the genome and aimed to investigate the effects of these mutations. In our previous study, the whole-genome sequence of the L. infantum_TR01 strain was obtained (Guldemir et al., 2020). In the present study, 3153 polymorphisms were detected in bioinformatics analysis performed on the Geneious 11.0.5. (www.geneious.com) platform. Herein, the L. infantum JPCM5 strain was used as the reference genome for genome mapping. Polymorphic regions were determined using the Find Variations/SNPs program on the Geneious platform. We further analyzed these polymorphisms detected in the previous study. Additionally, a literature review was performed by searching the PubMed database for proteins with polymorphisms. In our previous study (Guldemir et al., 2020), the genomic DNA sequence was submitted to the NCBI GenBank (www.ncbi.nlm.nih.gov) database and registered under the name Leishmania infantum_TR01 (Lin_TR01) and project accession number PRJNA437593. As a result of the annotation of the genome, 3153 polymorphisms were identified. In this study, 166 protein-coding polymorphisms were found among the 3153 polymorphisms, affecting 63 different proteins. Fourteen of them were studied, and the remaining 49 proteins were not studied. The 14 proteins examined in terms of the mutations detected in this study were related to virulence (n = 5), vaccine candidates (n = 2), diagnosis/typing (n = 4), drug resistance (n = 2), drug targets (n = 3) and vital function (n = 1). As mentioned previously, the acquisition of the Lin_TR01 genome was described in our previous study (Guldemir et al., 2020). The present meta-analytical study is the first comparison report of whole-genome sequence-based polymorphisms between the Turkish strain Leishmania infantum_TR01 and reference Leishmania infantum JPCM5 strain and evaluated polymorphisms and proteins. In this study, we focused on the mutations detected in the genome, and the effects of these mutations were investigated and evaluated together with the current literature. In our previous study, a high-quality WGS of Leishmania infantum was successfully obtained for the first time in Turkey (1). In this study, the comparison of both genomes will contribute to providing the scientific community with a solid infrastructure for postgenomic investigations of the parasite. •The present meta-analytical study is the first comparison report of WGS-based polymorphisms between the Lin_TR01 and reference strain.•This study is the first evaluated proteins with polymorphisms on Lin_TR01 genome.•In the present study, we focused on the mutations detected in the genome and aimed to investigate the effects of these mutations.•As a result of the annotation of the genome, 3153 polymorphisms were identified.•In this study, 166 protein-coding polymorphisms were found among the 3153 polymorphisms, affecting 63 different proteins.•In the pubmed literature search, it was found that only 14 of these 63 proteins were studied.•The 14 proteins examined in terms of the mutations detected in this study were related to virulence (n = 5), vaccine candidates (n = 2), diagnosis/typing (n = 4), drug resistance (n = 2), drug targets (n = 3) and vital function (n = 1).•In this study, the comparison of both genomes will contribute to providing the scientific community with a solid infrastructure for postgenomic investigations of the parasite.