Dataset Information

HV1 mtDNA Reveals the High Genetic Diversity and the Ancient Origin of Vietnamese Dogs.

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.

SUBMITTER: Thai QK

PROVIDER: S-EPMC10044065 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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HV1 mtDNA Reveals the High Genetic Diversity and the Ancient Origin of Vietnamese Dogs.

Thai Quan Ke QK Nguyen Thanh-Cong TC Le Cong-Trieu CT Chung Anh-Dung AD Nguyen Tran Minh-Ly TM Tran Quoc-Dung QD Savolainen Peter P Quan Quoc-Dang QD Tran Dai-Long DL Tran Hoang-Dung HD

Animals : an open access journal from MDPI 20230312 6

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 ...[more]

PMID: 36978577

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Project description:BackgroundCanine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes.DescriptionThe Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download.ConclusionsThe Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582 bp sequences.

Project description:In Pakistan, the origin of the indigenous cockfighting chicken (ICC) or gamecock population is unknown. However, it is speculated that this might have been associated with domestication, an event linked to recreational, entertainment (cockfighting), religious or ornamental activities. This study aims to understand the origin and genetic diversity of the ICC population in Pakistan. A total of 185 ICC population and 10 captive Indian red junglefowl (Gallus gallus murghi) were analyzed for genetic diversity indices and phylogenetic reconstruction using a 397 bp of mtDNA D-loop region. It is reported that a total of 43 haplotypes from 38 polymorphic nucleotide sites. The haplotype and nucleotide diversity are also estimated in the range of 0.643-0.909, and 0.00585-0.01575, respectively. The total genetic diversity within the population was 91.52%. Four mitochondrial haplogroups A, B, C and D were identified by median-joining network analysis, two of them have high percentages, haplogroup D (81.6%) and A (15.1%). Phylogenetic analysis showed that the ICC population of Pakistan and Gallus gallus murghi shared haplogroup D. The results of this study showed that sub-haplogroup D17a05, has significantly high haplotype diversity and percentage as compared to previously published studies, this indicated that Pakistan might be one of the centres of domestication for chicken, as it is considered that Southeast Asia is the centre of domestication. Frequencies of Haplogroup A also indicate South-North indices. This research work showed that the indigenous cockfighting chicken population of Pakistan is genetically introgressed from Gallus gallus murghi, and significant variations could be attributed to the underlying differences in the geographics, selection pressures, introgression, and regional practices; and multiple origins of cockfighting chickens' populations around the world which reflected the past trading routes between human communities and civilizations.

Dataset Information

HV1 mtDNA Reveals the High Genetic Diversity and the Ancient Origin of Vietnamese Dogs.

Publications

HV1 mtDNA Reveals the High Genetic Diversity and the Ancient Origin of Vietnamese Dogs.

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