Genetic Diversity in Hypervariable Segment I of Mitochondrial DNA Among the Kurdish Population Erbil City- Iraqi Kurdistan Region

Srwa yousif Anwer; Shakhawan Anwar Ali; Hazha Jamal Hidayat

doi:10.21271/ZJPAS.38.1.1

Authors

Srwa yousif Anwer Department of Biology, College of Education, Salahaddin University-Erbil, Kurdistan Region, Iraq
Shakhawan Anwar Ali Department of Pathological Analysis, Paytakht Technical Institute, Erbil-Kurdistan Region, IRAQ.
Hazha Jamal Hidayat Department of Biology, College of Education, Salahaddin University-Erbil, Kurdistan Region, Iraq

DOI:

https://doi.org/10.21271/ZJPAS.38.1.1

Keywords:

mtDNA, HVSI, Haplogroup prediction, Genetic diversity, Population origin

Abstract

Analysis of human sequence polymorphisms of mitochondrial DNA (mtDNA) hypervariable segment 1 (HV1) has become a significant technique in forensic casework and is used for genetic diversity and human evolution evaluation, consanguinity identification, and mitochondrial illness diagnosis. The present study aimed to provide insights into the demographic history and origins of the Kurdish people in the Iraqi Kurdistan region by analyzing mitochondrial DNA (mtDNA) sequence variations, particularly focusing on hypervariable segment 1 (HVS I). The HVS I of mtDNA was sequenced in 120 unrelated individuals from the Kurdish population by using Sangar sequencing. The study's findings reveal significant genetic diversity among the Kurdish population's HVS I of human mitochondrial DNA (mtDNA). The sequence of HVS I within the non-coding region had 413 mutations across 402 sites, resulting in 111 different haplotypes, as compared to the revised Cambridge Reference Sequence (rCRS) to gauge genetic diversity and community variety. Comparing this population sample to rCRS, the mutations found were (17.055%) transition and (0.921%) transversion. The phylogenetic tree for the Kurdistan region revealed a considerable degree of community variety. In order to determine the Kurdish ancestry and demographic history in the territory of Iraqi Kurdistan, the results also showed that the mtDNA haplotypes were classified into mtDNA haplogroups. The most frequent haplogroups were U, H, J, and HV, with frequencies of 22.5%, 19.2%, 14.5%, and 12.9%, respectively; nevertheless, T and N had a moderate prevalence of 8% and 6.4%, respectively. The haplotype results exhibited that Europe and India had the most genetic diversity in common with the Kurdish people of Iraqi Kurdistan. The findings will contribute to a better knowledge of Kurdish mitochondrial genome diversity, as well as to demographic history and forensic science.

References

ABU-AMERO, K. K., GONZÁLEZ, A. M., LARRUGA, J. M., BOSLEY, T. M. & CABRERA, V. M. 2007. Eurasian and African mitochondrial DNA influences in the Saudi Arabian population. BMC evolutionary biology, 7, 1-15.

AL-RASHEDI, N. A., JEBOR, M. A., MOUSA, T. A. & AL-SAADI, A. H. 2015. Mitochondrial DNA haplogroups observed in Iraqi population. Int J Sci Res, 4, 1424-1426.

AL-ZAHERY, N., PALA, M., BATTAGLIA, V., GRUGNI, V., HAMOD, M. A., KASHANI, B. H., OLIVIERI, A., TORRONI, A., SANTACHIARA-BENERECETTI, A. S. & SEMINO, O. 2011. In search of the genetic footprints of Sumerians: a survey of Y-chromosome and mtDNA variation in the Marsh Arabs of Iraq. BMC evolutionary biology, 11, 1-16.

AL-ZAHERY, N., SAUNIER, J., ELLINGSON, K., PARSON, W., PARSONS, T. J. & IRWIN, J. A. 2013. Characterization of mitochondrial DNA control region lineages in iraq. International journal of legal medicine, 127, 373-375.

ANDERSON, S., BANKIER, A. T., BARRELL, B. G., DE BRUIJN, M. H., COULSON, A. R., DROUIN, J., EPERON, I. C., NIERLICH, D. P., ROE, B. A. & SANGER, F. 1981. Sequence and organization of the human mitochondrial genome. Nature, 290, 457-465.

AZZAWI, B. I., OLEIWI, A. A., DARWEESH, M., JARADAT, S. & AL-ZAAG, A. 2013. Mitochondrial genome variation within Iraqi population. International Journal for Sciences and Technology, 8.

BEKTAS, Y., AKSU, I., KALAYCI, G. & BAYÇELEBİ, E. 2020. Low genetic diversity in Turkish populations of wels catfish Silurus glanis L., 1758 (Siluridae, Pisces) revealed by mitochondrial control region sequences. Turkish Journal of Fisheries and Aquatic Sciences, 20.

CLARK, J., REDDY, S., ZHENG, K., BETENSKY, R. A. & SIMON, D. K. 2011. Association of PGC-1alpha polymorphisms with age of onset and risk of Parkinson's disease. BMC medical genetics, 12, 1-9.

DATO, S., PASSARINO, G., ROSE, G., ALTOMARE, K., BELLIZZI, D., MARI, V., FERACO, E., FRANCESCHI, C. & DE BENEDICTIS, G. 2004. Association of the mitochondrial DNA haplogroup J with longevity is population specific. European journal of human genetics, 12, 1080-1082.

EXCOFFIER, L. & LISCHER, H. E. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular ecology resources, 10, 564-567.

FAN, L. & YAO, Y.-G. 2011. MitoTool: a web server for the analysis and retrieval of human mitochondrial DNA sequence variations. Mitochondrion, 11, 351-356.

FU, Y.-X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925.

HADI, I., ABDULLAH, M., JABER, A. & YOKE, C. 2014. Genetic variation of twenty autosomal STR loci and evaluate the importance of these loci for forensic genetic purposes. African Journal of Biotechnology, 13.

HALL, T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser., 1999. 95-98.

HAMEED, I. H., JEBOR, M. A. & KAREEM, M. A. 2015. Forensic analysis of mitochondrial DNA hypervariable region HVII (encompassing nucleotide positions 37 to 340) and HVIII (encompassing nucleotide positions 438-574) and evaluation of the importance of these variable positions for forensic genetic purposes. African Journal of Biotechnology, 14, 365-374.

HARPENDING, H. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human biology, 591-600.

JOHNSON, D. C., SHRESTHA, S., WIENER, H. W., MAKOWSKY, R., KURUNDKAR, A., WILSON, C. M. & AISSANI, B. 2015. Mitochondrial DNA diversity in the African American population. Mitochondrial DNA, 26, 445-451.

JOHNSON, S. M. 2013. Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations.

KAPOOR, V., ELK, M., TOLEDO-HERNANDEZ, C. & SANTO DOMINGO, J. W. 2017. Analysis of human mitochondrial DNA sequences from fecally polluted environmental waters as a tool to study population diversity. AIMS Environ Sci, 4, 443-455.

KIVISILD, T. 2015. Maternal ancestry and population history from whole mitochondrial genomes. Investigative genetics, 6, 1-10.

KIVISILD, T., ROOTSI, S., METSPALU, M., METSPALU, E., PARIK, J., KALDMA, K., USANGA, E., MASTANA, S., PAPIHA, S. S. & VILLEMS, R. 2003. The genetics of language and farming spread in India. Examining the farming/language dispersal hypothesis. McDonald Institute Monographs Series, McDonald Institute for Archaeological Research, Cambridge, UK, 215-222.

KLOSS‐BRANDSTÄTTER, A., PACHER, D., SCHÖNHERR, S., WEISSENSTEINER, H., BINNA, R., SPECHT, G. & KRONENBERG, F. 2011. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Human mutation, 32, 25-32.

KRISTJANSSON, D., SCHURR, T. G., BOHLIN, J. & JUGESSUR, A. 2023. Phylogeographic history of mitochondrial haplogroup J in Scandinavia. Am J Biol Anthropol, 180, 298-315.

KUMAR, S., NEI, M., DUDLEY, J. & TAMURA, K. 2008. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in bioinformatics, 9, 299-306.

KWAŚNIEWSKI, W., STUPAK, A., WAROWICKA, A., GOŹDZICKA-JÓZEFIAK, A., MOSIEWICZ, J. & MIECZKOWSKA, J. 2023. Mitochondrial DNA polymorphism in HV1 and HV2 regions and 12S rDNA in perimenopausal hypertensive women. Biomedicines, 11, 823.

MERGEN, H. 2004. Mitochondrial DNA sequence variation in the Anatolian Peninsula (Turkey). Journal of genetics, 83, 39-47.

NASIDZE, I., QUINQUE, D., OZTURK, M., BENDUKIDZE, N. & STONEKING, M. 2005. MtDNA and Y‐chromosome variation in Kurdish groups. Annals of human genetics, 69, 401-412.

NASIDZE, I., QUINQUE, D., RAHMANI, M., ALEMOHAMAD, S. A. & STONEKING, M. 2006. Concomitant replacement of language and mtDNA in South Caspian populations of Iran. Current Biology, 16, 668-673.

OHIED, B. M. & AL-BADRAN, A. I. 2020. Mitochondrial DNA (hypervariable region I) diversity in Basrah population–Iraq. Genomics, 112, 3560-3564.

PIERCY, R., SULLIVAN, K., BENSON, N. & GILL, P. 1993. The application of mitochondrial DNA typing to the study of white Caucasian genetic identification. International journal of legal medicine, 106, 85-90.

RICHARDS, M., MACAULAY, V., HICKEY, E., VEGA, E., SYKES, B., GUIDA, V., RENGO, C., SELLITTO, D., CRUCIANI, F. & KIVISILD, T. 2000. Tracing European founder lineages in the Near Eastern mtDNA pool. The American Journal of Human Genetics, 67, 1251-1276.

ROOSTALU, U., KUTUEV, I., LOOGVÄLI, E., METSPALU, E., TAMBETS, K., REIDLA, M., KHUSNUTDINOVA, E. K., USANGA, E., KIVISILD, T. & VILLEMS, R. 2007. Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective. Molecular biology and evolution, 24, 436-448.

RUIZ-PESINI, E., LOTT, M. T., PROCACCIO, V., POOLE, J. C., BRANDON, M. C., MISHMAR, D., YI, C., KREUZIGER, J., BALDI, P. & WALLACE, D. C. 2007. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic acids research, 35, D823-D828.

SAHAKYAN, H., HOOSHIAR KASHANI, B., TAMANG, R., KUSHNIAREVICH, A., FRANCIS, A., COSTA, M. D., PATHAK, A. K., KHACHATRYAN, Z., SHARMA, I., VAN OVEN, M., PARIK, J., HOVHANNISYAN, H., METSPALU, E., PENNARUN, E., KARMIN, M., TAMM, E., TAMBETS, K., BAHMANIMEHR, A., REISBERG, T., REIDLA, M., ACHILLI, A., OLIVIERI, A., GANDINI, F., PEREGO, U. A., AL-ZAHERY, N., HOUSHMAND, M., SANATI, M. H., SOARES, P., RAI, E., ŠARAC, J., ŠARIĆ, T., SHARMA, V., PEREIRA, L., FERNANDES, V., ČERNÝ, V., FARJADIAN, S., SINGH, D. P., AZAKLI, H., ÜSTEK, D., EKOMASOVA TROFIMOVA, N., KUTUEV, I., LITVINOV, S., BERMISHEVA, M., KHUSNUTDINOVA, E. K., RAI, N., SINGH, M., SINGH, V. K., REDDY, A. G., TOLK, H. V., CVJETAN, S., LAUC, L. B., RUDAN, P., MICHALODIMITRAKIS, E. N., ANAGNOU, N. P., PAPPA, K. I., GOLUBENKO, M. V., OREKHOV, V., BORINSKAYA, S. A., KALDMA, K., SCHAUER, M. A., SIMIONESCU, M., GUSAR, V., GRECHANINA, E., GOVINDARAJ, P., VOEVODA, M., DAMBA, L., SHARMA, S., SINGH, L., SEMINO, O., BEHAR, D. M., YEPISKOPOSYAN, L., RICHARDS, M. B., METSPALU, M., KIVISILD, T., THANGARAJ, K., ENDICOTT, P., CHAUBEY, G., TORRONI, A. & VILLEMS, R. 2017. Origin and spread of human mitochondrial DNA haplogroup U7. Sci Rep, 7, 46044.

SULTANA, G. N. N. & SULTAN, M. Z. 2018. Mitochondrial DNA and methods for forensic identification. J. Forensic. Sci. Crimin, Inves, 9.

TAJIMA, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.

TANG, H. 2002. Polymorphism of mtDNA HVR in Beijing Han population. Chinese J Forensic Med, 17, 32-33.

THEYAB, J. 2010. The Genetic Structure of the Kuwaiti Population: Mitochondrial DNA Markers. University of Kansas.

THEYAB, J. 2013. The Genetic Structure of the Kuwaiti and Failaka Island Populations: Y-chromosome & Mitochondrial DNA Variation. University of Kansas.

TRIKI-FENDRI, S., SÁNCHEZ-DIZ, P., REY-GONZÁLEZ, D., ALFADHLI, S., AYADI, I., BEN MARZOUG, R., CARRACEDO, Á. & REBAI, A. 2016. Genetic structure of the Kuwaiti population revealed by paternal lineages. Am J Hum Biol, 28, 203-12.

TSUTSUMI, H., MUKOYAMA, R. & KOMURO, T. 2004. Mitochondrial DNA polymorphism from dental pulp. DNA Polymorphism, 12, 249-251.

VAN OVEN, M. & KAYSER, M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Human mutation, 30, E386-E394.

VERMA, K., SHARMA, S., SHARMA, A., DALAL, J. & BHARDWAJ, T. 2018. Data on haplotype diversity in the hypervariable region I, II and III of mtDNA amongst the Brahmin population of Haryana. Data in brief, 17, 305-313.

WALSH, P. S., METZGER, D. A. & HIGUCHI, R. 1991. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques, 10, 506-513.

WARSHAUER, D. H., KING, J., EISENBERG, A. J. & BUDOWLE, B. 2013. Validation of the PLEX-ID TM mass spectrometry mitochondrial DNA assay. International journal of legal medicine, 127, 277-286.

YANG, Z. & YODER, A. D. 1999. Estimation of the transition/transversion rate bias and species sampling. Journal of Molecular Evolution, 48, 274-283.

ZAREI, F. & RAJABI-MAHAM, H. 2016. Phylogeography, genetic diversity and demographic history of the Iranian Kurdish groups based on mtDNA sequences. Journal of genetics, 95, 767-776.