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. 2017 Jun 26;18(1):60.
doi: 10.1186/s12863-017-0528-0.

Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database

Quan Ke Thai  1 , Dung Anh Chung  2 , Hoang-Dung Tran  3
Affiliations

Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database

Quan Ke Thai et al. BMC Genet. .

Abstract

Background: Canine 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.

Description: The 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.

Conclusions: The 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.

Keywords: Canis lupus familiaris; Control region; Database; HV1 haplotype; Haplotype identifier.

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Conflict of interest statement

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Polymorphic sites in the 582 bp region
Fig. 2
Fig. 2
Network formed by haplotypes in haplogroup C. The number by a link denotes the number of nucleotide differences between two haplotypes. Size of a node indicates the commonness of the corresponding haplotype in CHD
See this image and copyright information in PMC

References

    1. Vences M, Thomas M, van der Meijden A, Chiari Y, Vieites DR. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front Zool. 2005;2(1):5. doi: 10.1186/1742-9994-2-5. - DOI - PMC - PubMed
    1. Vila C, Savolainen P, Maldonado JE, Amorim IR, Rice JE, Honeycutt RL, Crandall KA, Lundeberg J, Wayne RK. Multiple and ancient origins of the domestic dog. Science. 1997;276(5319):1687–1689. doi: 10.1126/science.276.5319.1687. - DOI - PubMed
    1. Baute DT, Satkoski JA, Spear TF, Smith DG, Dayton MR, Malladi VS, Goyal V, Kou A, Kinaga JL, Kanthaswamy S. Analysis of forensic SNPs in the canine mtDNA HV1 mutational hotspot region. J Forensic Sci. 2008;53(6):1325–1333. - PubMed
    1. Yan L, Yaping Z. High genetic diversity of Tibetan mastiffs revealed by mtDNA sequences. Anim Genet. 2012;57(13):1483–1487.
    1. Gundry RL, Allard MW, Moretti TR, Honeycutt RL, Wilson MR, Monson KL, Foran DR. Mitochondrial DNA analysis of the domestic dog: control region variation within and among breeds. J Forensic Sci. 2007;52(3):562–572. doi: 10.1111/j.1556-4029.2007.00425.x. - DOI - PubMed

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