Whole-genome sequencing of a Toxoplasma gondii strain from a Turkish isolate using next-generation sequencing technology

Purpose: Toxoplasma gondii is an intracellular parasite that can affect all vertebrae and is the causative agent of toxoplasmosis. At present, the United States CDC (Centers for Disease Control and Prevention) recognizes this infection as a neglected disease. Toxoplasma gondii infection profiles exhibit differences because of the different regional and climatic responses to these parasites in Turkey, and these protozoan infections are notably common in this country. In this study, we attempted to obtain the whole-genome sequence of T. gondii using nextgeneration sequencing technology. Methods: Toxoplasma gondii isolates were isolated from an infant with congenital toxoplasmosis by Ekmen et al. (1974) in Ankara, Turkey. Whole-genome sequencing (WGS) was performed using the Illumina HiSeq 2500 and HiSeq SBS Kit v2. A T. gondii library was created on this device in the initial stage. After the completion of the library phase, sequence analysis was begun with a next-generation sequencing device. The resulting fragments were combined using paired-end (PE) reading and converted into a single DNA fragment. Bioinformatic analysis was performed using the Geneious 2.1. program. Results: In our study, WGS was successfully performed on T. gondii. The T. gondii whole-genome sequence has a coverage value of 50x, a size of 61,5763 Mb and a GC ratio of 52.6%. Data from this sequence were submitted to the National Center for Biotechnology Information (NCBI) GenBank (www.ncbi.nlm.nih.gov) database under the name Toxoplasma gondii TR01 (TG_TR01). The accession number of the genome obtained in this study is WOEV00000000.1. The biological sample access number is SAMN13338796. The genome of the T. gondii strain obtained in this study was compared with the reference genome, and 8312 CDSs (coding sequences), 183 tRNAs, 294 rRNAs and 8789 genes were identified. Among the 8312 CDSs, 4284 encoded hypothetical proteins (hypothetical protein CDSs/proteins of unknown function). The entire genome sequence of T gondii TR01 was compared with that of Toxoplasma gondii ME49. The results of this comparison demonstrate that the analyzed genome was 99,98% similar to the reference genome. The accession numbers of 14 chromosomes belonging to the genome sequences of T. gondii TR01 (TG_TR01) are CM019722.1, CM019723.1, CM019724.1, CM019725.1, CM019726.1, CM019727.1, CM019728.1, CM019729.1, CM019730.1, CM019731.1, CM019732.1, CM019733.1, CM019734.1, and CM019735.1. Conclusion: In this study, a whole-genome sequences of T. gondii was conducted for the first time in Turkey. The analyzed strain was named T. gondii TR01. The data obtained from this study may contribute to a better understanding of T. gondii. T. gondii is an important pathogen with an unusual population structure. Although T. gondii is highly zoonotic and has a complicated life cycle, some strains of this parasite have exhibited high genetic sequence similarity, and our study supports this knowlegde. The characterization of this strain may be very useful for the scientific community of our country and may help to establish a foundation for further research investigating the genome of T. gondii.