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Kunita F, Udagawa C, Inagaki T, Suzuki H, Bonkobara M, Omi T. Population genetics for 18 short tandem repeat loci (Canine Genotypes TM Panel 2.1 Kit) of 150 unrelated dogs from three pure-bred groups in Japan. Leg Med (Tokyo) 2024; 70:102472. [PMID: 38908212 DOI: 10.1016/j.legalmed.2024.102472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/16/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024]
Abstract
Similar to that in Europe and the United States, the need for forensic DNA identification in dogs is increasing in Japan. As few studies have used commercial genotyping kits, the effectiveness of the Canine GenotypesTM Panel 2.1 Kit for individual DNA identification in dogs bred in Japan was examined. We genotyped 150 unrelated dogs (50 Golden Retrievers, 50 Miniature Dachshunds, and 50 Shiba Inu) at 18 canine short tandem repeat loci by the Kit. The allele frequency, expected heterozygosity, observed heterozygosity, p-value, power of the discriminant, and of exclusion, polymorphic information content, and random matching probability were calculated for each marker. The random matching probability was subsequently estimated to be 4.394×10-22 in the 150 dogs of the three pure-bred groups based on 18 STR loci; 3.257 × 10-16 in the Golden Retriever, 3.933 × 10-18 in the Miniature Dachshund, and 2.107 × 10-18 in the Shiba Inu breeds. In addition, principal component analysis based on genotype data revealed the Golden Retrievers, Miniature Dachshunds, and Shiba Inus separated into three clusters. The results of the genotype analysis showed that the Canine GenotypesTM Panel 2.1 Kit could be useful for identity testing and tool of population study of canines in Japan.
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Affiliation(s)
- Fubuki Kunita
- Faculty of Veterinary Medicine, School of Veterinary Nursing and Technology, Department of Basic Science, Nippon Veterinary and Life Science University, Musashino-Shi, Tokyo 180-8602, Japan
| | - Chihiro Udagawa
- Faculty of Veterinary Medicine, School of Veterinary Nursing and Technology, Department of Basic Science, Nippon Veterinary and Life Science University, Musashino-Shi, Tokyo 180-8602, Japan
| | - Takeshi Inagaki
- Department of Legal Medicine, Jichi Medical University, Shimotuske-shi, Tochgi-ken 329-0498, Japan
| | - Hideto Suzuki
- Department of Legal Medicine, Jichi Medical University, Shimotuske-shi, Tochgi-ken 329-0498, Japan
| | - Makoto Bonkobara
- Faculty of Veterinary Medicine, School of Veterinary Medicine, Department of Veterinary Clinical Pathology, Nippon Veterinary and Life Science University, Musashino-shi, Tokyo 180-8602, Japan; Research Center for Animal Life Science, Nippon Veterinary and Life Science University, Musashino-Shi, Tokyo 180-8602, Japan
| | - Toshinori Omi
- Faculty of Veterinary Medicine, School of Veterinary Nursing and Technology, Department of Basic Science, Nippon Veterinary and Life Science University, Musashino-Shi, Tokyo 180-8602, Japan; Department of Legal Medicine, Jichi Medical University, Shimotuske-shi, Tochgi-ken 329-0498, Japan; Research Center for Animal Life Science, Nippon Veterinary and Life Science University, Musashino-Shi, Tokyo 180-8602, Japan.
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Thai QK, Nguyen TC, Le CT, Chung AD, Nguyen TML, Tran QD, Savolainen P, Quan QD, Tran DL, Tran HD. HV1 mtDNA Reveals the High Genetic Diversity and the Ancient Origin of Vietnamese Dogs. Animals (Basel) 2023; 13:ani13061036. [PMID: 36978577 PMCID: PMC10044065 DOI: 10.3390/ani13061036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/14/2023] Open
Abstract
In this study, samples from 429 dog individuals across three main regions of Vietnam (Southern Vietnam (SVN), Central Vietnam (CVN), and Northern Vietnam (NVN)) were collected to analyze the 582 bp region mtDNA HVI, so as to study the genetic diversity and to screen the rare haplotype E in the Vietnamese village dog population. Nine new haplotypes A, two new haplotypes B, and three haplotypes C were unique to Vietnam dogs, in which the new haplotypes An3, An7, Cn1, and Cn3 concerned mutations at new polymorphism sites (15,517, 15,505, 15,479, and 15,933, respectively) which have not been previously reported. The detection of haplotypes A9 and A29, and the appearance of haplotype A200 in the two individual dogs sampled support that the Southeast Asian dog is the ancestor of today’s Australian dingo and Polynesian dog. The two rare haplotypes E (E1 and E4) were reconfirmed in Vietnamese dogs and discussed. This study also contributes to strengthening the theory of domestication of dogs to the south of the Yangtze River and the Southeast Asian origin of the dingo.
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Affiliation(s)
- Quan Ke Thai
- Faculty of Natural science Education, Saigon University, 273 An Duong Vuong, Ward 3, District 5, Ho Chi Minh City 72710, Vietnam
- Correspondence: (Q.K.T.); (H.-D.T.); Tel.: +84-918-297-640 (Q.K.T.); +84-772-999-537 (H-D.T.)
| | - Thanh-Cong Nguyen
- Faculty of Biotechnology, Nguyen-Tat-Thanh University, 298A-300A Nguyen-Tat-Thanh Street, District 04, Ho Chi Minh City 72820, Vietnam
| | - Cong-Trieu Le
- Soc Trang Vocational College, 176 Nam Ky Khoi Nghia Street, Ward 7, Soc Trang City 96114, Vietnam
| | - Anh-Dung Chung
- Biotechnology Division, Institute of Agricultural Sciences for Southern Viet Nam, 121 Nguyen Binh Khiem Street, Da Kao Ward, 1st District, Ho Chi Minh City 710302, Vietnam
| | - Tran Minh-Ly Nguyen
- Faculty of Business Administration, TU Bergakademie Freiberg, Akademiestraße 6, 09599 Freiberg, Germany
| | - Quoc-Dung Tran
- Faculty of Biology, University of Education, Hue University, 34 Le 5Loi Street, Hue City 49118, Vietnam
| | - Peter Savolainen
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), 171 65 Solna, Sweden
| | - Quoc-Dang Quan
- Agency for Southern Affairs of Ministry of Science and Technology, 31 Han Thuyen Street, Ben Nghe Ward, District 1, Ho Chi Minh City 70055, Vietnam
| | - Dai-Long Tran
- Department of Supervisor Inspector, Van Lang University, Nguyen Khac Nhu Street, Co Giang Ward, Distric 1, Ho Chi Minh City 700000, Vietnam
| | - Hoang-Dung Tran
- Faculty of Biology and Environment, Ho Chi Minh City University of Food Industry, 140 Le Trong Tan Street, Tay Thanh Ward, Tan Phu District, Ho Chi Minh City 72009, Vietnam
- Institute of Applied Research and Technology Transfer HUFI, Ho Chi Minh City University of Food Industry, 140 Le Trong Tan Street, Tay Thanh Ward, Tan Phu District, Ho Chi Minh City 72009, Vietnam
- Correspondence: (Q.K.T.); (H.-D.T.); Tel.: +84-918-297-640 (Q.K.T.); +84-772-999-537 (H-D.T.)
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Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs. Genes (Basel) 2023; 14:genes14030650. [PMID: 36980922 PMCID: PMC10048372 DOI: 10.3390/genes14030650] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Bernese mountain dogs are a large dog breed formed in the early 1900s in Switzerland. While originally farm dogs that were used for pulling carts, guarding, and driving cattle, today they are considered multi-purpose companion and family dogs. The breed is predisposed to several complex diseases, such as histiocytic sarcoma, degenerative myelopathy, or hip dysplasia. Using whole-genome sequencing (WGS) data, we assessed the genomic architecture of 33 unrelated dogs from four countries: France, Sweden, Switzerland, and the United States. Analysis of runs of homozygosity (ROH) identified 12,643 ROH with an average length of 2.29 Mb and an average inbreeding coefficient of 0.395. Multidimensional scaling analysis of the genetic relatedness revealed limited clustering of European versus USA dogs, suggesting exchanges of breeding stock between continents. Furthermore, only two mtDNA haplotypes were detected in the 33 studied dogs, both of which are widespread throughout multiple dog breeds. WGS-based ROH analyses revealed several fixed or nearly fixed regions harboring discreet morphological trait-associated as well as disease-associated genetic variants. Several genes involved in the regulation of immune cells were found in the ROH shared by all dogs, which is notable in the context of the breed’s strong predisposition to hematopoietic cancers. High levels of inbreeding and relatedness, strongly exaggerated in the last 30 years, have likely led to the high prevalence of specific genetic disorders in this breed.
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Perini F, Cardinali I, Ceccobelli S, Gruppetta A, José CS, Cosenza M, Musso N, Martìnez A, Abushady AM, Monteagudo LV, Liotta L, Lancioni H, Attard G, Lasagna E. Phylogeographic and population genetic structure of hound-like native dogs of the Mediterranean Basin. Res Vet Sci 2023; 155:103-114. [PMID: 36669378 DOI: 10.1016/j.rvsc.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/02/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
The dog was probably the first domesticated animal. Despite extensive archaeological and genetic investigations, the origin and the evolution of the extant dogs are still being debated. Dog breeds that have over time been selected for hunting share common ancestral traits. This study represents the first comprehensive attempt to survey at the genomic and mitochondrial level eight hound-like dogs breeds indigenous to the Mediterranean Basin to determine if they share common ancient origins. Results from the microsatellite analysis indicate that all the dog populations have a low inbreeding value.The Kelb tal-Fenek has a high divergence from the current Egyptian street population, however there is not enough evidence from this study to exclude completely the potential of an ancient common relationship. Overall, the mitochondrial results indicate high frequencies of haplogroups A and B and a low representation of haplogroup C, while only one Egyptian dog could be assigned to haplogroup D. Results reveal identities and shared clades, suggesting the conservation of ancient European mitotypes in the Mediterranean hound-like breeds, especially in the Egyptian population. Although none of the dog populations/breeds participating in this study indicate to be direct descendants of the Egyptian dogs, they still have a very close morphologically resemblance to those iconic Egyptian dogs often depicted in ancient art forms and share some genetic links with the current Egyptian population. Further research is required with other markers such us complete mitogenomes and SNP panels to confirm the complex history of the Mediterranean dogs involved in this study.
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Affiliation(s)
- Francesco Perini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto, 06123 Perugia, Italy
| | - Simone Ceccobelli
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche 10, 60131 Ancona, Italy.
| | - Anthony Gruppetta
- St. Simon Veterinary Practice, 53, Grognet Street MST 3611, Mosta, Northern Region, Malta
| | - Carlos San José
- Biodonostia Health Research Institute, Paseo Dr. Begiristain, s/n, 20014 San Sebastián, Gipuzkoa, Spain
| | - Mario Cosenza
- Laboratorio di Genetica Forense Veterinaria, Unirelab srl, Milan, Settimo Milanese, Italy
| | - Nicolò Musso
- Molecular Analysis and Biology Laboratory Biogene, Via Giacomo Leopardi 50, 95127 Catania, Italy
| | - Amparo Martìnez
- Department of Genetics, University of Córdoba, Ctra. Madrid-Córdoba km 396, 14071 Córdoba, Spain
| | - Asmaa M Abushady
- Biotechnology School, Nile University, first 6th of October, Giza Governorate, Egypt; Department of Genetics, Faculty of Agriculture, Ain Shams University, Shubra Al Kheimah, Awal Shubra Al Kheimah, Cairo, Egypt
| | - Luis V Monteagudo
- Department of Anatomy, Embryology and Animal Genetics, Faculty of Veterinary Sciences, University of Zaragoza, Calle de Pedro Cerbuna, 12, 50009 Zaragoza, Spain; Agrifood Institute of Aragon (IA2), University of Zaragoza-CITA, Calle de Pedro Cerbuna, 12, 50009 Zaragoza, Spain
| | - Luigi Liotta
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto, 06123 Perugia, Italy
| | - George Attard
- Department of Rural Sciences and Food Systems, University of Malta, 2080 Msida, Malta
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
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Evaluation of the tRNA-Leu (UUR) gene haplotype profile observed in canine mammary gland tumours based on comparative analysis with the MT-TL1 human gene. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The aetiology and pathogenesis of many canine tumours are likely to be similar to cancers found in humans. This study aimed to evaluate a plausible link between changes in the tRNA-Leu (UUR) gene and the carcinogenesis process in dogs with mammary gland tumours. The whole mitochondrial DNA (mtDNA) isolated from blood and tumour tissues of 13 dogs with malignant mammary gland tumours was sequenced. The present work is the first report showing that some polymorphisms might occur at the corresponding positions in the human and canine mtDNA genome, which in turn may provoke similar deleterious effects. The homology between the human MT-TL1 and canine tRNA-Leu (UUR) genes was 84%. After resequencing of the whole mitochondrial DNA genome with the use of the NGS technology, two polymorphisms in two haplotypes were identified: m.2683G>A (observed in 18 out of 27 samples) and m.2678_2679insG (27 out of 27 samples). The m.2683G>A polymorphism corresponded to a deleterious change at m.3243A>G, which is linked with MELAS (Mitochondrial Encephalomyopathy, Lactic Acidosis, Stroke-like episodes) syndrome and with different types of cancers in humans as well. The comparative analysis of MT-TL1 and tRNA-Leu (UUR) led us to hypothesise that the m.2678_2679insG and m.2683G>A polymorphisms might influence the dog’s condition and might be linked with tumourigenesis, as observed in humans.
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Kowal K, Tkaczyk-Wlizło A, Pierzchała M, Gawor J, Ślaska B. Molecular differences in mitochondrial DNA genomes of dogs with malignant mammary tumours. Vet Comp Oncol 2021; 20:256-264. [PMID: 34554638 DOI: 10.1111/vco.12772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 07/01/2021] [Accepted: 09/20/2021] [Indexed: 11/30/2022]
Abstract
The aim of this study was to determine molecular defects in mitochondrial DNA (mtDNA) with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained from 13 dogs with mammary gland tumours. The total number of mutations and polymorphisms in the analysed mitochondrial genomes was 557. We identified 383 single nucleotide polymorphisms (SNP), 32 indels (or length polymorphisms), 4 mutations, 137 heteroplasmic positions and 1 indel mutation. The highest variability (132 changes) was observed in the variable number of tandem repeats (VNTR) region. The heteroplasmy rate in VNTR varied among individuals and even between two tumours in one organism. Our previous study resulted in determination of a probable CpG island in this region, thus it is not excluded that these changes might alter mtDNA methylation. Only the ATP8 gene was not affected by any polymorphisms or mutations, whereas the COX1 gene had the highest number of polymorphisms from all protein-coding genes. One change m.13594G>A was detected in a region spanning two genes: ND5 and ND6, from which a deleterious effect was observed for the ND5 protein. Molecular changes were frequently observed in the TΨC loop, which is thought to interact with ribosomal RNA.
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Affiliation(s)
- Krzysztof Kowal
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Angelika Tkaczyk-Wlizło
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Mariusz Pierzchała
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Brygida Ślaska
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
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Development of a mitochondrial DNA marker that distinguishes domestic dogs from Washington state gray wolves. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01130-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Analysis of Mitochondrial Genome from Labrador (Canis lupus familiaris) with Mammary Gland Tumour Reveals Novel Mutations and Polymorphisms. ANNALS OF ANIMAL SCIENCE 2019. [DOI: 10.2478/aoas-2019-0027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The aim of the study was to find associations between the process of neoplastic transformation and mtDNA mutations/polymorphisms, i.e. factors with potential prognostic significance, and to determine their impact on the biochemical properties, as well as structural, and functional properties of proteins. Blood and neoplastic tissue samples were collected from a 9-year-old Labrador dog with a diagnosed malignant mammary tumour. Next-generation genome sequencing (NGS) of the entire mitochondrial genome was performed using Illumina technology, and bioinformatics analyses were carried out. This is the first report demonstrating the application of NGS in the analysis of the canine mtDNA genome in neoplastic disease. The proposed strategy is innovative and promising. For the first time in the literature, the sequence of 29 genes was analysed to determine their association with the prevalence of tumour. In total, 32 polymorphic loci and 15 mutations were identified. For the first time, as many as 24 polymorphisms and all the mutations have been described to be associated with the neoplastic process in dogs. Most polymorphisms/mutations were found in the D-loop (31% of the polymorphisms and 93% of the mutations) and the COX1 gene sequence (16% of the polymorphisms). Blood or cancer heteroplasmy was noted in 93% of the mutations. Four of the 18 polymorphisms detected in the protein-coding genes were non-synonymous polymorphisms that have not been described in the literature so far (m.T7593C in COX2, m.G8807A in COX3, m.A9911G in ND4L, and m.T13299A in ND5) but resulted in changes in amino acids in proteins. These mutations and polymorphisms can affect mitochondrial functions and may be a result of cell adaptation to the changes in the environment occurring during carcinogenesis. The replacement of “wild type” mtDNA by a mutated molecule may be an important phenomenon accompanying carcinogenesis.
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Marinov M, Teofanova D, Gadjev D, Radoslavov G, Hristov P. Mitochondrial diversity of Bulgarian native dogs suggests dual phylogenetic origin. PeerJ 2018; 6:e5060. [PMID: 29967734 PMCID: PMC6026455 DOI: 10.7717/peerj.5060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/04/2018] [Indexed: 11/20/2022] Open
Abstract
The dog has been the first domesticated animal to have a central role in human society from ancient times to present day. Although there have been numerous investigations of dog phylogeny and origin, genetic data of dogs in the region of the Balkan Peninsula (South-Eastern Europe) are still scarce. Therefore, the aim of the present study was to perform phylogenetic analysis of three native Bulgarian dog breeds. A total of 130 samples were analyzed at HVR1 (hypervariable region, D-loop region). The samples were taken from two hunting dog breeds (Bulgarian Hound Dog: Barak, n = 34; Bulgarian Scenthound Dog: Gonche, n = 45) as well as from a Bulgarian Shepherd Dog (n = 51). The first two breeds are reared in a flat region of the country (the Northern part of Bulgaria, the Danubian Plain), while the last breed is a typical representative of the mountainous part of the country. The results have shown the presence of almost all main clades—A, B, C and D—in the three dog breeds taken together, except clades E and F, as expected. With regard to haplogroups distribution, there are clear differences among investigated breeds. While hunting breeds exhibit a prevalence of clade C, the mountainous Shepherd dog shows presence of the D2 haplogroup but absence of the C clade. In conclusion, the present study has been the first to investigate the mitochondrial DNA diversity of native dog breeds in Bulgaria. The results have revealed a clear difference of haplogroups dissemination in native hunting and shepherd dogs, which suggests a dual independent phylogenetic origin, without hybridization events between these dogs.
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Affiliation(s)
- Miroslav Marinov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Denitsa Teofanova
- Department of Biochemistry, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Dimitar Gadjev
- Agricultural and Stockbreeding Experimental Station, Agricultural Academy, Smolyan, Bulgaria
| | - Georgi Radoslavov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Peter Hristov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Ren Z, Chen H, Yang X, Zhang C. Phylogenetic analysis of Tibetan mastiffs based on mitochondrial hypervariable region I. J Genet 2017; 96:119-125. [PMID: 28360396 DOI: 10.1007/s12041-017-0753-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Recently, the number of Tibetan mastiffs, which is a precious germplasm resource and cultural heritage, is decreasing sharply. Therefore, the genetic diversity of Tibetan mastiffs needs to be studied to clarify its phylogenetics relationships and lay the foundation for resource protection, rational development and utilization of Tibetan mastiffs. We sequenced hypervariable region I of mitochondrial DNA (mtDNA) of 110 individuals from Tibet region and Gansu province. A total of 12 polymorphic sites were identified which defined eight haplotypes of which H4 and H8 were unique to Tibetan population with H8 being identified first. The haplotype diversity (Hd: 0.808), nucleotide diversity (Pi: 0.603%), the average number of nucleotide difference (K: 3.917) of Tibetan mastiffs from Gansu were higher than those from Tibet region (Hd: 0.794; Pi: 0.589%; K: 3.831), which revealed higher genetic diversity in Gansu. In terms of total population, the genetic variation was low. The median-joining network and phylogenetic tree based on the mtDNA hypervariable region I showed that Tibetan mastiffs originated from grey wolves, as the other domestic dogs and had different history of maternal origin. The mismatch distribution analysis and neutrality tests indicated that Tibetan mastiffs were in genetic equilibrium or in a population decline.
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Affiliation(s)
- Zhanjun Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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Banes GL, Galdikas BMF. Effective Characterisation of the Complete Orang-Utan Mitochondrial DNA Control Region, in the Face of Persistent Focus in Many Taxa on Shorter Hypervariable Regions. PLoS One 2016; 11:e0168715. [PMID: 28033350 PMCID: PMC5199090 DOI: 10.1371/journal.pone.0168715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/04/2016] [Indexed: 11/18/2022] Open
Abstract
The hypervariable region I (HVRI) is persistently used to discern haplotypes, to distinguish geographic subpopulations, and to infer taxonomy in a range of organisms. Numerous studies have highlighted greater heterogeneity elsewhere in the mitochondrial DNA control region, however-particularly, in some species, in other understudied hypervariable regions. To assess the abundance and utility of such potential variations in orang-utans, we characterised 36 complete control-region haplotypes, of which 13 were of Sumatran and 23 of Bornean maternal ancestry, and compared polymorphisms within these and within shorter HVRI segments predominantly analysed in prior phylogenetic studies of Sumatran (~385 bp) and Bornean (~323 bp) orang-utans. We amplified the complete control region in a single PCR that proved successful even with highly degraded, non-invasive samples. By using species-specific primers to produce a single large amplicon (~1600 bp) comprising flanking coding regions, our method also serves to better avoid amplification of nuclear mitochondrial insertions (numts). We found the number, length and position of hypervariable regions is inconsistent between orang-utan species, and that prior definitions of the HVRI were haphazard. Polymorphisms occurring outside the predominantly analysed segments were phylogeographically informative in isolation, and could be used to assign haplotypes to comparable clades concordant with geographic subpopulations. The predominantly analysed segments could discern only up to 76% of all haplotypes, highlighting the forensic utility of complete control-region sequences. In the face of declining sequencing costs and our proven application to poor-quality DNA extracts, we see no reason to ever amplify only specific 'hypervariable regions' in any taxa, particularly as their lengths and positions are inconsistent and cannot be reliably defined-yet this strategy predominates widely. Given their greater utility and consistency, we instead advocate analysis of complete control-region sequences in future studies, where any shorter segment might otherwise have proven the region of choice.
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Affiliation(s)
- Graham L. Banes
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- CAS-MPG Partner Institute for Computational Biology, Shanghai, People’s Republic of China
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12
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Surdyka M, Slaska B. Defect of the mitochondrial DNA hypervariable region as a risk factor for canine mammary tumour. Vet Comp Oncol 2016; 15:820-828. [PMID: 27198058 DOI: 10.1111/vco.12224] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/05/2016] [Accepted: 02/07/2016] [Indexed: 12/12/2022]
Abstract
The aim of this study was to identify mutations in the hypervariable region of mitochondrial DNA in canine mammary tumours and to determine their association with the process of neoplastic transformation. A total of 93 biological samples, including blood as well as normal and neoplastic tissue samples from 31 dogs with diagnosed malignant canine mammary tumours were analysed. DNA extraction, amplification and sequencing of the D-loop as well as bioinformatic and statistical analyses were performed. In the mitochondrial D-loop sequence, 26 polymorphic loci and 5 mutations were identified. For the first time, D-loop length heteroplasmy was detected in dogs with mammary tumours. The malignancy grade exerted no effect on the presence of nucleotide changes. A statistically significant association between the presence of mutations and polymorphisms and the size of dogs was demonstrated. The 100% frequency of length heteroplasmy may imply that this is a hotspot mutation of canine mammary tumour.
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Affiliation(s)
- M Surdyka
- Department of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - B Slaska
- Department of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
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13
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Aksöyek E, İbiş O, Özcan S, Moradi M, Tez C. DNA barcoding of three species (Canis aureus, Canis lupus and Vulpes vulpes) of Canidae. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:747-755. [PMID: 27180732 DOI: 10.1080/24701394.2016.1180512] [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] [Indexed: 10/21/2022]
Abstract
Sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene have been used for DNA barcoding and determining the genetic diversity of mammal species. In the current study, our intention was to test the validity of COI barcodes for detecting genetic divergence and to reveal whether or not there is a genetic variation at this marker within canids. Three species (Canis aureus, Canis lupus and Vulpes vulpes) from the family Canidae were selected for DNA barcoding using samples collected from Iran and Turkey. All three species had unique barcoding sequences and none of the sequences were shared among these species. The mean sequence divergences within and among the species were 0.61% and 12.32%, respectively, which fell into the mean divergence ranges found in some mammal groups. The genetic diversity of these three canid species was relatively higher than that found in previously reported studies.
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Affiliation(s)
- Eren Aksöyek
- a Graduate School of Natural and Applied Sciences , Erciyes University , Kayseri , Turkey
| | - Osman İbiş
- b Department of Agricultural Biotechnology, Faculty of Agriculture , Erciyes University , Kayseri , Turkey.,c Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey
| | - Servet Özcan
- c Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey.,d Department of Biology, Faculty of Sciences , Erciyes University , Kayseri , Turkey
| | - Mohammad Moradi
- e Department of Biology, Faculty of Science , University of Zanjan , Zanjan , Iran
| | - Coşkun Tez
- d Department of Biology, Faculty of Sciences , Erciyes University , Kayseri , Turkey
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14
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Śmiech A, Ślaska B, Surdyka M, Grzybowska-Szatkowska L, Łopuszyński W, Różańska D. Identification of additional mitochondrial DNA mutations in canine mast cell tumours. Acta Vet Scand 2016; 58:28. [PMID: 27146669 PMCID: PMC4855722 DOI: 10.1186/s13028-016-0210-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 04/24/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Research has revealed the presence of somatic mutations in mitochondrial DNA (mtDNA) of certain types of tumours. As this has not been studied for canine mast cell tumours, the aim of this study was to identify mutations in the hypervariable region of mtDNA in mast cell tumours in dogs and determine their association with the process of neoplastic transformation. RESULTS Samples from 17 dogs with histopathologically confirmed mast cell tumours were analysed. The samples consisted of tumour tissues (n = 17), normal tissues (n = 17), and blood (n = 17). Amplicons of the displacement loop (D-loop) were sequenced and the obtained nucleotide sequences were subjected to bioinformatics analyses. Somatic mutations were detected in seven positions of the D-loop nucleotide sequences in 47 % of the dogs, while polymorphisms were identified in 94 % of the dogs. Most of these changes were homoplasmic, while heteroplasmy was detected in two individuals. Six new haplotypes were established as being characteristic for canine mast cell tumours. There was no association between the presence of the mutations and sex, haplotype, or malignancy grade assessed in 3 and 2-grade scales. CONCLUSIONS Differences in the frequency of somatic mutations imply their direct association with the neoplastic transformation. However, their functional consequences and clinical significance are not clear. The mutations may be used for diagnosis and prognosis of canine mast cell tumours in the future.
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15
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Complete mitochondrial genome database and standardized classification system for Canis lupus familiaris. Forensic Sci Int Genet 2015. [PMID: 26218982 DOI: 10.1016/j.fsigen.2015.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To contribute to the complete mitogenome database of the species Canis lupus familiaris and shed more light on its origin, we have sequenced mitochondrial genomes of 120 modern dogs from worldwide populations. Together with all the previously published mitogenome sequences of acceptable quality, we have reconstructed a global phylogenetic tree of 555 C. l. familiaris mitogenomes and standardized haplogroup nomenclature. The phylogenetic tree presented here and available online at http://clf.mtdna.tree.cm.umk.pl/ could be further used by forensic and evolutionary geneticists as well cynologists, for data quality control and unambiguous haplogroup classification. Our in-depth phylogeographic analysis of all C. l. familiaris mitogenomes confirmed that domestic dogs may have originated in East Asia during the Mesolithic and Upper Paleolithic time periods and started to expand to other parts of the world during Neolithic times.
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16
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Blackie R, Taylor D, Linacre A. Successful direct amplification of nuclear markers from single dog hairs using DogFiler multiplex. Electrophoresis 2015; 36:2082-5. [DOI: 10.1002/elps.201400560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/22/2015] [Accepted: 04/24/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Renée Blackie
- School of Biological Sciences; Flinders University; Adelaide SA Australia
| | - Duncan Taylor
- School of Biological Sciences; Flinders University; Adelaide SA Australia
- Forensic Science South Australia; Adelaide SA Australia
| | - Adrian Linacre
- School of Biological Sciences; Flinders University; Adelaide SA Australia
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17
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Brown SK, Darwent CM, Wictum EJ, Sacks BN. Using multiple markers to elucidate the ancient, historical and modern relationships among North American Arctic dog breeds. Heredity (Edinb) 2015; 115:488-95. [PMID: 26103948 DOI: 10.1038/hdy.2015.49] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 03/17/2015] [Accepted: 04/28/2015] [Indexed: 11/09/2022] Open
Abstract
Throughout most of the Americas, post-colonial dogs largely erased the genetic signatures of pre-historical dogs. However, the North American Arctic harbors dogs that are potentially descended from pre-historical ancestors, as well as those affected by post-colonial translocations and admixtures. In particular, Inuit dogs from Canada and Greenland are thought to descend from dogs associated with Thule peoples, who relied on them for transportation ca. 1000 years ago. Whether Thule dogs reflected an earlier colonization by Paleoeskimo dogs ca. 4500 years ago is unknown. During the Alaskan Gold Rush, additional sled dogs, possibly of post-colonial derivation, the Alaskan Husky, Malamute and Siberian Husky, were used in the Arctic. The genealogical relationships among and origins of these breeds are unknown. Here we use autosomal, paternal and maternal DNA markers to (1) test the hypothesis that Inuit dogs have retained their indigenous ancestry, (2) characterize their relationship to one another and to other Arctic breeds, and (3) estimate the age of North American indigenous matrilines and patrilines. On the basis of the agreement of all three markers we determined that Inuit dogs have maintained their indigenous nature, and that they likely derive from Thule dogs. In addition, we provide support for previous research that the Inuit dogs from Canada and Greenland dog should not be distinguished as two breeds. The Alaskan Husky displayed evidence of European introgression, in contrast to the Malamute and Siberian Husky, which appear to have maintained most of their ancient Siberian ancestry.
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Affiliation(s)
- S K Brown
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, CA, USA.,Department of Anthropology, University of California, Davis, CA, USA
| | - C M Darwent
- Department of Anthropology, University of California, Davis, CA, USA
| | - E J Wictum
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, CA, USA
| | - B N Sacks
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, CA, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
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18
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Fregel R, Suárez NM, Betancor E, González AM, Cabrera VM, Pestano J. Mitochondrial DNA haplogroup phylogeny of the dog: Proposal for a cladistic nomenclature. Mitochondrion 2015; 22:75-84. [PMID: 25869968 DOI: 10.1016/j.mito.2015.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 09/27/2014] [Accepted: 04/02/2015] [Indexed: 10/23/2022]
Abstract
Canis lupus familiaris mitochondrial DNA analysis has increased in recent years, not only for the purpose of deciphering dog domestication but also for forensic genetic studies or breed characterization. The resultant accumulation of data has increased the need for a normalized and phylogenetic-based nomenclature like those provided for human maternal lineages. Although a standardized classification has been proposed, haplotype names within clades have been assigned gradually without considering the evolutionary history of dog mtDNA. Moreover, this classification is based only on the D-loop region, proven to be insufficient for phylogenetic purposes due to its high number of recurrent mutations and the lack of relevant information present in the coding region. In this study, we design 1) a refined mtDNA cladistic nomenclature from a phylogenetic tree based on complete sequences, classifying dog maternal lineages into haplogroups defined by specific diagnostic mutations, and 2) a coding region SNP analysis that allows a more accurate classification into haplogroups when combined with D-loop sequencing, thus improving the phylogenetic information obtained in dog mitochondrial DNA studies.
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Affiliation(s)
- Rosa Fregel
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain; Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain.
| | - Nicolás M Suárez
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Eva Betancor
- Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas, Spain
| | - Ana M González
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain
| | - Vicente M Cabrera
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain
| | - José Pestano
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain; Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas, Spain
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19
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Peng MS, Fan L, Shi NN, Ning T, Yao YG, Murphy RW, Wang WZ, Zhang YP. DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals. Mol Ecol Resour 2015; 15:1238-42. [PMID: 25655564 DOI: 10.1111/1755-0998.12386] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/01/2015] [Accepted: 02/02/2015] [Indexed: 01/01/2023]
Abstract
Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up-to-date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high-resolution mtDNA haplogroup trees based on 1240 complete or near-complete mtDNA genome sequences are available in open resource DomeTree (http://www.dometree.org). In addition, we offer the software MitoToolPy (http://www.mitotool.org/mp.html) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Long Fan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999077, China
| | - Ni-Ni Shi
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Tiao Ning
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Yong-Gang Yao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, M5S 2C6, Canada
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.,Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
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20
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Spadaro A, Ream K, Braham C, Webb KM. Local mitochondrial DNA haplotype databases needed for domestic dog populations that have experienced founder effect. Forensic Sci Int 2015; 248:113-8. [PMID: 25612881 DOI: 10.1016/j.forsciint.2014.12.025] [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: 08/06/2014] [Revised: 11/19/2014] [Accepted: 12/27/2014] [Indexed: 10/24/2022]
Abstract
Biological material from pets is often collected as evidence from crime scenes. Due to sample type and quality, mitochondrial DNA (mtDNA) is frequently evaluated to identify the potential contributor. MtDNA has a lower discriminatory power than nuclear DNA with multiple individuals in a population potentially carrying the same mtDNA sequence, or haplotype. The frequency distribution of mtDNA haplotypes in a population must be known in order to determine the evidentiary value of a match between crime scene evidence and the potential contributor of the biological material. This is especially important in geographic areas that include remote and/or isolated populations where founder effect may have lead to a decrease in genetic diversity and a non-random distribution of haplotypes relative to the population at large. Here we compared the haplotype diversity in dogs from the noncontiguous states of Alaska and Hawaii relative to the contiguous United States (US). We report a greater proportion of dogs carrying an A haplotype in Alaska relative to any other US population. Significant variation in the distribution of haplotype frequencies was discovered when comparing the haplotype diversity of dogs in Hawaii to that of the continental US. Each of these regions exhibits reduced genetic diversity relative to the contiguous US, likely due to founder effect. We recommend that specific databases be created to accurately represent the mitochondrial haplotype diversity in these remote areas. Furthermore, our work demonstrates the importance of local surveys for populations that may have experienced found effect.
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Affiliation(s)
- Amanda Spadaro
- Department of Biology, Allegheny College, Meadville, PA, United States
| | - Kelsey Ream
- Department of Natural Resources and Environmental Science, University of Illinois, Urbana, IL, United States
| | - Caitlyn Braham
- Department of Graduate Studies, John Carroll University, University Heights, OH, United States
| | - Kristen M Webb
- Department of Biology, Allegheny College, Meadville, PA, United States.
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21
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Verscheure S, Backeljau T, Desmyter S. Coding region SNP analysis to enhance dog mtDNA discrimination power in forensic casework. Forensic Sci Int Genet 2014; 14:86-95. [PMID: 25299153 DOI: 10.1016/j.fsigen.2014.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/30/2014] [Accepted: 09/07/2014] [Indexed: 11/26/2022]
Abstract
The high population frequencies of three control region haplotypes contribute to the low discrimination power of the dog mtDNA control region. It also diminishes the evidential power of a match with one of these haplotypes in forensic casework. A mitochondrial genome study of 214 Belgian dogs suggested 26 polymorphic coding region sites that successfully resolved dogs with the three most frequent control region haplotypes. In this study, three SNP assays were developed to determine the identity of the 26 informative sites. The control region of 132 newly sampled dogs was sequenced and added to the study of 214 dogs. The assays were applied to 58 dogs of the haplotypes of interest, which confirmed their suitability for enhancing dog mtDNA discrimination power. In the Belgian population study of 346 dogs, the set of 26 sites divided the dogs into 25 clusters of mtGenome sequences with substantially lower population frequency estimates than their control region sequences. In case of a match with one of the three control region haplotypes, using these three SNP assays in conjunction with control region sequencing would augment the exclusion probability of dog mtDNA analysis from 92.9% to 97.0%.
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Affiliation(s)
- Sophie Verscheure
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120 Brussels, Belgium; University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Thierry Backeljau
- University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020 Antwerp, Belgium; Royal Belgian Institute of Natural Sciences (OD "Taxonomy and Phylogeny" and JEMU), Vautierstraat 29, B-1000 Brussels, Belgium
| | - Stijn Desmyter
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120 Brussels, Belgium
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22
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Pilli E, Casamassima R, Vai S, Virgili A, Barni F, D’Errico G, Berti A, Lago G, Caramelli D. Pet fur or fake fur? A forensic approach. INVESTIGATIVE GENETICS 2014; 5:7. [PMID: 24991403 PMCID: PMC4079164 DOI: 10.1186/2041-2223-5-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/29/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND In forensic science there are many types of crime that involve animals. Therefore, the identification of the species has become an essential investigative tool. The exhibits obtained from such offences are very often a challenge for forensic experts. Indeed, most biological materials are traces, hair or tanned fur. With hair samples, a common forensic approach should proceed from morphological and structural microscopic examination to DNA analysis. However, the microscopy of hair requires a lot of experience and a suitable comparative database to be able to recognize with a high degree of accuracy that a sample comes from a particular species and then to determine whether it is a protected one. DNA analysis offers the best opportunity to answer the question, 'What species is this?' In our work, we analyzed different samples of fur coming from China used to make hats and collars. Initially, the samples were examined under a microscope, then the mitochondrial DNA was tested for species identification. For this purpose, the genetic markers used were the 12S and 16S ribosomal RNA, while the hypervariable segment I of the control region was analyzed afterwards, to determine whether samples belonged to the same individual. RESULTS Microscopic examination showed that the fibres were of animal origin, although it was difficult to determine with a high degree of confidence which species they belonged to and if they came from a protected species. Therefore, DNA analysis was essential to try to clarify the species of these fur samples. CONCLUSIONS Macroscopic and microscopic analysis confirmed the hypothesis regarding the analyzed hair belonging to real animals, although it failed to prove with any kind of certainty which actual family it came from, therefore, the species remains unknown. Sequence data analysis and comparisons with the samples available in GenBank showed that the hair, in most cases, belonged to the Canidae family, and in one case only to Felidae.
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Affiliation(s)
- Elena Pilli
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Florence, Italy
| | - Rosario Casamassima
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Chimica, viale Tor di Quinto 119, Rome, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Florence, Italy
| | - Antonino Virgili
- Istituto Superiore di Tecniche Investigative dei Carabinieri, viale Salvo D’Acquisto 2, 00049 Velletri (Roma), Italy
| | - Filippo Barni
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Rome, Italy
| | - Giancarlo D’Errico
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Rome, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Rome, Italy
| | - Giampietro Lago
- Reparto Carabinieri Investigazioni Scientifiche di Parma, Parco Ducale 3, Parma, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Florence, Italy
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23
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Angleby H, Oskarsson M, Pang J, Zhang YP, Leitner T, Braham C, Arvestad L, Lundeberg J, Webb KM, Savolainen P. Forensic informativity of ~3000 bp of coding sequence of domestic dog mtDNA. J Forensic Sci 2014; 59:898-908. [PMID: 24814664 DOI: 10.1111/1556-4029.12504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 05/10/2013] [Indexed: 11/30/2022]
Abstract
The discriminatory power of the noncoding control region (CR) of domestic dog mitochondrial DNA alone is relatively low. The extent to which the discriminatory power could be increased by analyzing additional highly variable coding regions of the mitochondrial genome (mtGenome) was therefore investigated. Genetic variability across the mtGenome was evaluated by phylogenetic analysis, and the three most variable ~1 kb coding regions identified. We then sampled 100 Swedish dogs to represent breeds in accordance with their frequency in the Swedish population. A previously published dataset of 59 dog mtGenomes collected in the United States was also analyzed. Inclusion of the three coding regions increased the exclusion capacity considerably for the Swedish sample, from 0.920 for the CR alone to 0.964 for all four regions. The number of mtDNA types among all 159 dogs increased from 41 to 72, the four most frequent CR haplotypes being resolved into 22 different haplotypes.
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Affiliation(s)
- Helen Angleby
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, School of Biotechnology, SE-171 65, Solna, Sweden
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24
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Verscheure S, Backeljau T, Desmyter S. Dog mitochondrial genome sequencing to enhance dog mtDNA discrimination power in forensic casework. Forensic Sci Int Genet 2014; 12:60-8. [PMID: 24905334 DOI: 10.1016/j.fsigen.2014.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/02/2014] [Indexed: 11/26/2022]
Abstract
A Belgian dog population sample and several population studies worldwide have confirmed that only a limited number of mtDNA control region haplotypes is observed in the majority of dogs. The high population frequency of these haplotypes negatively impacts both the exclusion probability of dog mtDNA analysis and the evidential value of a match with one of these haplotypes in casework. Variation within the mtDNA coding region was explored to improve the discrimination power of dog mtDNA analysis. In the current study, the entire mitochondrial genome of 161 dogs was sequenced applying a quality assured strategy and resulted in a total of 119 different mitochondrial genome sequences. Our research was focused on those dogs with the six most common control region haplotypes from a previous Belgian population study. We identified 33 informative SNPs that successfully divide the six most common control region haplotypes into 32 clusters of mitochondrial genome sequences. Determining the identity of these 33 polymorphic sites in addition to control region sequencing in case of a match with one of these 6 control region haplotypes could augment the exclusion probability of forensic dog mtDNA analysis from 92.5% to 97.5%.
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Affiliation(s)
- Sophie Verscheure
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120 Brussels, Belgium; University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Thierry Backeljau
- University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020 Antwerp, Belgium; Royal Belgian Institute of Natural Sciences (OD "Taxonomy and Phylogeny" and JEMU), Vautierstraat 29, B-1000 Brussels, Belgium
| | - Stijn Desmyter
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120 Brussels, Belgium
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25
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Spicer AM, Kun TJ, Sacks BN, Wictum EJ. Mitochondrial DNA sequence heteroplasmy levels in domestic dog hair. Forensic Sci Int Genet 2014; 11:7-12. [PMID: 24631692 DOI: 10.1016/j.fsigen.2014.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 02/01/2014] [Accepted: 02/13/2014] [Indexed: 11/25/2022]
Abstract
To assess the level of mtDNA sequence heteroplasmy in dog hair, we sequenced a 612 base pair fragment of the hypervariable region 1 (HVI) in 576 hairs from six dogs representing a range of age, sex, breed, and hair color. Blood and buccal samples were collected from each dog for reference. Three instances of sequence heteroplasmy were observed at nucleotide positions 15627 (G/A), 15628 (T/C) and 15639 (G/A) in two hairs from different dogs. An HVI sequence heteroplasmy frequency of 0.0034 was obtained. The Probability of Identity (PI) value, or probability that two random, unrelated dog hairs share an HVI sequence, and the Power of Discrimination (PD), or probability that two random unrelated dog hairs have different HVI sequences, were determined from the 88 HVI haplotypes represented in the Veterinary Genetics Laboratory database (n=1006) and found to be 0.086 and 0.914, respectively.
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Affiliation(s)
- Ashley M Spicer
- Forensic Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Teri J Kun
- Forensic Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Benjamin N Sacks
- Canid Diversity and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Elizabeth J Wictum
- Forensic Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA.
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26
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Jia QH, Liu HB, Gu XL, Li JF, Liu YL. Complete mitochondrial genome of a German Shepherd (Canis lupus familiaris breed German Shepherd) provides insights into genome-wide sequence variations. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:118-9. [PMID: 24438283 DOI: 10.3109/19401736.2013.873930] [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] [Indexed: 11/13/2022]
Abstract
In this work, we report the complete mitochondrial genome sequence of a German shepherd. The total length of the mitogenome was 16,727 bp. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region (D-loop region). The arrangement of these genes was the same as that found in other dogs. All the protein initial codons were ATG, except for ND2, ND3 and ND5 starting with ATA. Sequence comparison indicates that D-loop region harbors most sequence variations.
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Affiliation(s)
- Qing-Hui Jia
- a Key Laboratory of Preventive Veterinary Medicine in Hebei Province , Hebei Normal University of Science and Technology , Qinhuangdao , China
| | - Hong-Bin Liu
- b Department of pharmacy , Hebei North University , Zhangjiakou , China
| | - Xiao-Long Gu
- c Department of Animal Science and Technology , Hebei North University , Zhangjiakou , China , and
| | - Jie-Feng Li
- d Department of Animal Science , Institute of Animal Science of Hebei , Baoding , China
| | - Yan-Long Liu
- a Key Laboratory of Preventive Veterinary Medicine in Hebei Province , Hebei Normal University of Science and Technology , Qinhuangdao , China
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27
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Verscheure S, Backeljau T, Desmyter S. Reviewing population studies for forensic purposes: Dog mitochondrial DNA. Zookeys 2013:381-411. [PMID: 24453568 PMCID: PMC3890688 DOI: 10.3897/zookeys.365.5859] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 12/14/2013] [Indexed: 02/02/2023] Open
Abstract
The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype’s population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework.
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Affiliation(s)
- Sophie Verscheure
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium ; University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020, Antwerp, Belgium
| | - Thierry Backeljau
- University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020, Antwerp, Belgium ; Royal Belgian Institute of Natural Sciences (OD "Taxonomy and Phylogeny" and JEMU), Vautierstraat 29, B-1000, Brussels, Belgium
| | - Stijn Desmyter
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
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Analysis of mitochondrial DNA HVR1 haplotype of pure-bred domestic dogs in Japan. Leg Med (Tokyo) 2013; 15:303-9. [PMID: 24120304 DOI: 10.1016/j.legalmed.2013.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 11/20/2022]
Abstract
To develop DNA markers for forensic analysis, we examined the hypervariable region 1 (HVR1) sequences of 447 pure-bred domestic dogs (Canis lupus familiaris) that had been bred and raised in Japan. HVR1 is a 660-bp stretch of mitochondrial (mt) DNA. Among the 447 HVR1 sequences examined, we identified 58 haplotypes from 47 single nucleotide polymorphisms (SNPs) and two insertion-deletion (InDel) polymorphisms. The haplotype diversity inferred from inter-breed analysis (N=154, 88 breeds) was 0.929±0.011. Intra-breed analysis showed that the haplotype diversity of Golden Retrievers (N=53), Labrador Retrievers (N=67), Miniature Dachshunds (N=61), Toy Poodles (N=62), and Welsh Corgis (N=50) was 0.624±0.052, 0.722±0.029, 0.922±0.010, 0.877±0.020, and 0.443±0.084, respectively. The results of this genotype analysis were used to construct a dataset consisting of dog mtDNA HVR1 sequences for use in forensic applications in Japan.
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Imes DL, Wictum EJ, Allard MW, Sacks BN. Identification of single nucleotide polymorphisms within the mtDNA genome of the domestic dog to discriminate individuals with common HVI haplotypes. Forensic Sci Int Genet 2012; 6:630-9. [PMID: 22436122 DOI: 10.1016/j.fsigen.2012.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 02/08/2012] [Accepted: 02/09/2012] [Indexed: 11/26/2022]
Abstract
We sequenced the entire ∼16 kb canine mitochondrial genome (mtGenome) of 100 unrelated domestic dogs (Canis lupus familiaris) and compared these to 246 published sequences to assess hypervariable region I (HVI) haplotype frequencies. We then used all available sequences to identify informative single nucleotide polymorphisms (SNPs) outside of the control region for use in further resolving mtDNA haplotypes corresponding to common HVI haplotypes. Haplotype frequencies in our data set were highly correlated with previous ones (e.g., F(ST)=0.02, r=0.90), suggesting the total data set reasonably reflected the broader dog population. A total of 128 HVI haplotypes was represented. The 10 most common HVI haplotypes (n=184 dogs) represented 53.3% of the sample. We identified a total 71 SNPs in the mtGenomes (external to the control region) that resolved the 10 most common HVI haplotypes into 63 mtGenome subhaplotypes. The random match probability of the dataset based solely on the HVI sequence was 4%, whereas the random match probability of the mtGenome subhaplotypes was <1%. Thus, the panel of 71 SNPs identified in this study represents a useful forensic tool to further resolve the identity of individual dogs from mitochondrial DNA (mtDNA).
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Affiliation(s)
- Donna L Imes
- Canid Diversity and Conservation Laboratory, Center for Veterinary Genetics, University of California at Davis, Davis, CA 95616, USA.
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