Genome mutations of the Turkish strain Leishmania infantum_TR01.

PURPOSE: 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. METHODS: 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. RESULTS: 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). CONCLUSION: 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.

Genome Sequencing of Leishmania infantum Causing Cutaneous Leishmaniosis from a Turkish Isolate with Next-Generation Sequencing Technology.

PURPOSE: Leishmania subgenus Leishmania causes leishmaniosis, which is a chronic systemic disease in humans and animals, in which the skin and visceral organs can be affected. The disease generally consists of three different clinical types in humans: visceral (kala-azar, VL), cutaneous (CL) and mucocutaneous leishmaniosis (MCL). According to the World Health Organization (WHO), leishmaniosis is still one of the world's most neglected diseases. It has been nearly 13-14 years since the completion of the first complete genome sequence of a Leishmania parasite. However, much information about these parasites remains to be elucidated, such as the causes of differences in tissue tropism. The aim of this study is to perform the whole-genome sequencing of Leishmania infantum causing cutaneous leishmaniosis from a Turkish isolate with next-generation sequencing technology. METHODS: Genomic sequencing was performed on the Illumina HiSeq 2500 platform. The TruSeq Nano DNA Low Throughput Library Prep Kit, compatible with the Illumina HiSeq 2500 platform, was used to generate the library. Synthesis sequencing (SBS) was performed with a HiSeq Rapid SBS Kit v2 to generate single-fragment reads (2 × 150 bp; PE) with two fragment end-to-end assemblies. Bioinformatics analyses were performed on the Geneious 11.0.5. ( www.genius.com ) platform. RESULTS: In our study, a high-quality whole-genome sequence (WGS) of L. infantum was successfully generated, and a total of 32,009,137 base pairs of genomic DNA from 36 chromosomes were obtained. The resulting genomic DNA sequence was submitted to the US National Center for Biotechnology Information (NCBI) GenBank ( www.ncbi.nlm.nih.gov ) database and registered under the name Leishmania infantum_TR01 (Lin_TR01). The following accession numbers were assigned by NCBI to the 36 chromosomes of the Lin_TR01 genome: CP027807, CP027810, CP027808, CP027811, CP027809, CP027812, CP027813, CP027814, CP027817, CP027818, CP027819, CP027815, CP027821, CP027816, CP027823, CP027820, CP027822, CP027824, CP027825, CP027826, CP027827, CP027828, CP027829, CP027830, CP027831, CP027832, CP027833, CP027834, CP027835, CP027836, CP027837, CP027838, CP027839, CP027840, CP027841, CP027842. As a result of the annotation of the Lin_TR01 genome, 3153 polymorphisms, 8324 genes, 8199 CDSs, 8109 mRNAs, 67 tRNAs, 11 rRNAs and 58 ncRNA were identified. Among the 8199 CDS obtained, 5278 encode hypothetical proteins. CONCLUSION: In this study, a high-quality WGS of Leishmania infantum was successfully obtained for the first time in Turkey. According to a review of WGS studies on this subject, the Lin_TR01 strain is the first strain to be isolated from cutaneous leishmaniosis. The reference genome of L. infantum JPCM5 (Peacock et al., 2007) was obtained from a visceral leishmaniosis case, in accordance with the classical tissue and organ tropism of the species. Lin_TR01 is the second whole-genome-sequenced strain in the world after the JPCM5 strain. The Lin_TR01 genome is the only L. infantum whole-genome sequence that is completed assembly level from 36 chromosomes among the genomes obtained thus far ( https://www.ncbi.nlm.nih.gov/genome/genomes/249 ).