Helena's Many Daughters: More Mitogenome Diversity Behind the Most Common West Eurasian MtDNA Control Region Haplotype in an Extended Italian Population Sample

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2022 Jun 24

PMID 35743173

Authors

Martin Bodner

Christina Amory

Anna Olivieri

Francesca Gandini

Irene Cardinali

Hovirag Lancioni

Gabriela Huber

Catarina Xavier

Maria Pala

Alessandro Fichera

Lisa Schnaller

Mario Gysi

Stefania Sarno

Davide Pettener

Donata Luiselli

Martin B Richards

Ornella Semino

Alessandro Achilli

Antonio Torroni

Walther Parson

Affiliations

Soon will be listed here.

Abstract

The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.

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References

Parsons T, Coble M . Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial DNA genome. Croat Med J. 2001; 42(3):304-9. View

Bar W, Brinkmann B, Budowle B, Carracedo A, Gill P, Holland M . Guidelines for mitochondrial DNA typing. DNA Commission of the International Society for Forensic Genetics. Vox Sang. 2000; 79(2):121-5. DOI: 10.1159/000031227. View

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D . Circos: an information aesthetic for comparative genomics. Genome Res. 2009; 19(9):1639-45. PMC: 2752132. DOI: 10.1101/gr.092759.109. View

Parolo S, Lisa A, Gentilini D, Di Blasio A, Barlera S, Nicolis E . Characterization of the biological processes shaping the genetic structure of the Italian population. BMC Genet. 2015; 16:132. PMC: 4640365. DOI: 10.1186/s12863-015-0293-x. View

Achilli A, Rengo C, Magri C, Battaglia V, Olivieri A, Scozzari R . The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet. 2004; 75(5):910-8. PMC: 1182122. DOI: 10.1086/425590. View

Fiorito G, Di Gaetano C, Guarrera S, Rosa F, Feldman M, Piazza A . The Italian genome reflects the history of Europe and the Mediterranean basin. Eur J Hum Genet. 2015; 24(7):1056-62. PMC: 5070887. DOI: 10.1038/ejhg.2015.233. View

Babalini C, Martinez-Labarga C, Tolk H, Kivisild T, Giampaolo R, Tarsi T . The population history of the Croatian linguistic minority of Molise (southern Italy): a maternal view. Eur J Hum Genet. 2005; 13(8):902-12. DOI: 10.1038/sj.ejhg.5201439. View

Berger C, Hatzer-Grubwieser P, Hohoff C, Parson W . Evaluating sequence-derived mtDNA length heteroplasmy by amplicon size analysis. Forensic Sci Int Genet. 2010; 5(2):142-5. PMC: 3064993. DOI: 10.1016/j.fsigen.2010.10.002. View

Nilsson M, Andreasson-Jansson H, Ingman M, Allen M . Evaluation of mitochondrial DNA coding region assays for increased discrimination in forensic analysis. Forensic Sci Int Genet. 2008; 2(1):1-8. DOI: 10.1016/j.fsigen.2007.07.004. View

10.

Coia V, Boschi I, Trombetta F, Cavulli F, Montinaro F, Destro-Bisol G . Evidence of high genetic variation among linguistically diverse populations on a micro-geographic scale: a case study of the Italian Alps. J Hum Genet. 2012; 57(4):254-60. DOI: 10.1038/jhg.2012.14. View

11.

Tagliabracci A, Turchi C, Buscemi L, Sassaroli C . Polymorphism of the mitochondrial DNA control region in Italians. Int J Legal Med. 2001; 114(4-5):224-8. DOI: 10.1007/s004140000168. View

12.

Garcia O, Alonso S, Huber N, Bodner M, Parson W . Forensically relevant phylogeographic evaluation of mitogenome variation in the Basque Country. Forensic Sci Int Genet. 2020; 46:102260. DOI: 10.1016/j.fsigen.2020.102260. View

13.

Lippold S, Xu H, Ko A, Li M, Renaud G, Butthof A . Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. Investig Genet. 2014; 5:13. PMC: 4174254. DOI: 10.1186/2041-2223-5-13. View

14.

Just R, Leney M, Barritt S, Los C, Smith B, Holland T . The use of mitochondrial DNA single nucleotide polymorphisms to assist in the resolution of three challenging forensic cases. J Forensic Sci. 2009; 54(4):887-91. DOI: 10.1111/j.1556-4029.2009.01069.x. View

15.

Silva M, Oteo-Garcia G, Martiniano R, Guimaraes J, von Tersch M, Madour A . Biomolecular insights into North African-related ancestry, mobility and diet in eleventh-century Al-Andalus. Sci Rep. 2021; 11(1):18121. PMC: 8438022. DOI: 10.1038/s41598-021-95996-3. View

16.

Just R, Scheible M, Fast S, Sturk-Andreaggi K, Rock A, Bush J . Full mtGenome reference data: development and characterization of 588 forensic-quality haplotypes representing three U.S. populations. Forensic Sci Int Genet. 2014; 14:141-55. DOI: 10.1016/j.fsigen.2014.09.021. View

17.

Parson W, Dur A . EMPOP--a forensic mtDNA database. Forensic Sci Int Genet. 2008; 1(2):88-92. DOI: 10.1016/j.fsigen.2007.01.018. View

18.

Parson W, Huber G, Moreno L, Madel M, Brandhagen M, Nagl S . Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples. Forensic Sci Int Genet. 2014; 15:8-15. DOI: 10.1016/j.fsigen.2014.11.009. View

19.

Pereira L, Soares P, Radivojac P, Li B, Samuels D . Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity. Am J Hum Genet. 2011; 88(4):433-9. PMC: 3071914. DOI: 10.1016/j.ajhg.2011.03.006. View

20.

Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P . Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata. PLoS One. 2013; 8(5):e65441. PMC: 3666984. DOI: 10.1371/journal.pone.0065441. View