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Patterson EC, Lall GM, Neumann R, Ottolini B, Batini C, Sacchini F, Foster AP, Wetton JH, Jobling MA. Mitogenome sequences of domestic cats demonstrate lineage expansions and dynamic mutation processes in a mitochondrial minisatellite. BMC Genomics 2023; 24:690. [PMID: 37978434 PMCID: PMC10655372 DOI: 10.1186/s12864-023-09789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND As a population genetic tool, mitochondrial DNA is commonly divided into the ~ 1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes. RESULTS To increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes in our dataset) and defines a phylogeny showing similar starlike topologies within all major clades (haplogroups), likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups. CONCLUSIONS In defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion.
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Affiliation(s)
- Emily C Patterson
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Gurdeep Matharu Lall
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Barbara Ottolini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Oxford Nanopore Technologies Plc., Oxford Science Park, Edmund Halley Rd, Oxford, OX4 4DQ, UK
| | - Chiara Batini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Department of Population Health Sciences, University of Leicester, Leicester, UK
- Biomedical Research Centre, Leicester National Institute for Health and Care Research, Glenfield Hospital, Leicester, UK
| | - Federico Sacchini
- IDEXX Laboratories Italia S.R.L., Via Guglielmo Silva, 36-20149, Milano, MI, Italy
| | - Aiden P Foster
- Bristol Veterinary School, University of Bristol, Langford House, Langford, BS40 5DU, North Somerset, UK
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Patterson EC, Lall GM, Neumann R, Ottolini B, Sacchini F, Foster AP, Jobling MA, Wetton JH. Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing. Forensic Sci Int Genet 2023; 67:102944. [PMID: 37820546 DOI: 10.1016/j.fsigen.2023.102944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
Hair shed by domestic cats is a potentially useful source of forensic evidence. Analysable hair DNA is predominantly mitochondrial, but the recent domestication history of cats means that mtDNA diversity is low. A 402-bp control region segment is usually sequenced, defining only a small number of distinct haplotypes in populations. Previously, we used a long-amplicon approach to sequence whole mitogenomes in a sample of blood DNAs from 119 UK cats, greatly increasing observed diversity and reducing random match probabilities. To exploit this variation for forensic analysis, we here describe a multiplex system that amplifies the cat mitogenome in 60 overlapping amplicons of mean length 360 bp, followed by Nanopore sequencing. Variants detected in multiplex sequence data from unrooted hair completely mirror those from long-amplicon data from blood from the same individuals. However, applying the multiplex to matched blood DNA reveals additional sequence variants which derive from the major feline nuclear mitochondrial insertion sequence (numt), which covers 7.9 kb of the 17-kb mitogenome and exists in multiple tandem copies. We use long-amplicon Nanopore sequencing to investigate numt variation in a set of cats, together with an analysis of published genome sequences, and show that numt arrays are variable in both structure and sequence, thus providing a potential source of uncertainty when nuclear DNA predominates in a sample. Forensic application of the multiplex was demonstrated by matching hairs from a cat with skeletal remains from its putative mother, both of which shared a globally common haplotype at the control region. The random match probability in this case with the CR 402-bp segment was 0.21 and this decreased to 0.03 when considering the whole mitogenome. The developed multiplex and sequencing approach, when applied to cat hair where nuclear DNA is scarce, can provide a reliable and highly discriminating source of forensic genetic evidence from a single hair. The confounding effect of numt co-amplification in degraded samples where mixed sequences are observed can be mitigated by variant phasing, and by comparison with numt sequence diversity data, such as those presented here.
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Affiliation(s)
- Emily C Patterson
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Gurdeep Matharu Lall
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Barbara Ottolini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Federico Sacchini
- IDEXX Laboratories Italia S.r.l., Via Guglielmo Silva, 36-20149 Milano (MI), Italy
| | - Aiden P Foster
- Bristol Veterinary School, University of Bristol, Langford House, Langford, North Somerset BS40 5DU, UK
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.
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Cardinali I, Tancredi D, Lancioni H. The Revolution of Animal Genomics in Forensic Sciences. Int J Mol Sci 2023; 24:ijms24108821. [PMID: 37240167 DOI: 10.3390/ijms24108821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Nowadays, the coexistence between humans and domestic animals (especially dogs and cats) has become a common scenario of daily life. Consequently, during a forensic investigation in civil or criminal cases, the biological material from a domestic animal could be considered "evidence" by law enforcement agencies. Animal genomics offers an important contribution in attacks and episodes of property destruction or in a crime scene where the non-human biological material is linked to the victim or perpetrator. However, only a few animal genetics laboratories in the world are able to carry out a valid forensic analysis, adhering to standards and guidelines that ensure the admissibility of data before a court of law. Today, forensic sciences focus on animal genetics considering all domestic species through the analysis of STRs (short tandem repeats) and autosomal and mitochondrial DNA SNPs (single nucleotide polymorphisms). However, the application of these molecular markers to wildlife seems to have gradually gained a strong relevance, aiming to tackle illegal traffic, avoid the loss of biodiversity, and protect endangered species. The development of third-generation sequencing technologies has glimmered new possibilities by bringing "the laboratory into the field", with a reduction of both the enormous cost management of samples and the degradation of the biological material.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Domenico Tancredi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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McCord BR, Gauthier Q, Cho S, Roig MN, Gibson-Daw GC, Young B, Taglia F, Zapico SC, Mariot RF, Lee SB, Duncan G. Forensic DNA Analysis. Anal Chem 2019; 91:673-688. [PMID: 30485738 DOI: 10.1021/acs.analchem.8b05318] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bruce R McCord
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Quentin Gauthier
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sohee Cho
- Department of Forensic Medicine , Seoul National University , Seoul , 08826 , South Korea
| | - Meghan N Roig
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Georgiana C Gibson-Daw
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Brian Young
- Niche Vision, Inc. , Akron , Ohio 44311 , United States
| | - Fabiana Taglia
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sara C Zapico
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Roberta Fogliatto Mariot
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Steven B Lee
- Forensic Science Program, Justice Studies Department , San Jose State University , San Jose , California 95192 , United States
| | - George Duncan
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
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Wesselink M, Desmyter S, Kuiper I. Local populations and inaccuracies: Determining the relevant mitochondrial haplotype distributions for North West European cats. Forensic Sci Int Genet 2017. [DOI: 10.1016/j.fsigen.2017.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ottolini B, Lall GM, Sacchini F, Jobling MA, Wetton JH. Application of a mitochondrial DNA control region frequency database for UK domestic cats. Forensic Sci Int Genet 2017; 27:149-155. [PMID: 28073089 DOI: 10.1016/j.fsigen.2016.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/21/2016] [Accepted: 12/19/2016] [Indexed: 11/15/2022]
Abstract
DNA variation in 402bp of the mitochondrial control region flanked by repeat sequences RS2 and RS3 was evaluated by Sanger sequencing in 152 English domestic cats, in order to determine the significance of matching DNA sequences between hairs found with a victim's body and the suspect's pet cat. Whilst 95% of English cats possessed one of the twelve globally widespread mitotypes, four new variants were observed, the most common of which (2% frequency) was shared with the evidential samples. No significant difference in mitotype frequency was seen between 32 individuals from the locality of the crime and 120 additional cats from the rest of England, suggesting a lack of local population structure. However, significant differences were observed in comparison with frequencies in other countries, including the closely neighbouring Netherlands, highlighting the importance of appropriate genetic databases when determining the evidential significance of mitochondrial DNA evidence.
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Affiliation(s)
- Barbara Ottolini
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Gurdeep Matharu Lall
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Federico Sacchini
- IDEXX Laboratories Ltd., Grange House, Sandbeck Way, Wetherby, West Yorkshire, LS22 7DN, UK
| | - Mark A Jobling
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK.
| | - Jon H Wetton
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK; School of History, University of Leicester, University Road, Leicester LE1 7RH, UK.
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Głażewska I, Kijewski T. A new view on the European feline population from mtDNA analysis in Polish domestic cats. Forensic Sci Int Genet 2017; 27:116-122. [PMID: 28068530 DOI: 10.1016/j.fsigen.2016.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/22/2016] [Accepted: 12/27/2016] [Indexed: 10/20/2022]
Abstract
Domestic cats from Eastern Europe have been poorly represented in studies on mitochondrial DNA diversity for forensic purposes until now. The aim of the present study was to contribute to closing this gap. The genetic structure and the origin of a cat population in Poland were examined against the background of human migrations over the centuries. One hundred and eighty-one cats from animal shelters in seven cities were genotyped. Twenty-one mtDNA haplotypes were found, with only one haplotype present in each of the populations, at an average frequency of 63.54%, and 13 haplotypes being found only in single populations. The analysis revealed the unexpectedly high frequency of haplotype PL02, in previous studies observed only in single cats. Differences in the number of the haplotypes, from four to eight, were observed among the shelters. The findings are discussed with regard to a world-wide database of feline sequences and to the complicated history of Poland. The study underscores the necessity of creating local databases of haplotypes that are of high evidentiary value to the forensic investigations conducted in a given country.
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Affiliation(s)
- Iwona Głażewska
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Tomasz Kijewski
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland.
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