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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-017-0528-0) contains supplementary material, which is available to authorized users.

Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains

“…The longer fragment recovered from OWW9 confirmed the above-mentioned correlations with modern samples, but it was not possible to compare it with ancient specimens due to their shorter fragments available. Given the results obtained, the analyses on this sample were nonetheless aimed at deepening the phylogenetic relationship with dogs, which highlighted that this haplotype fall within the canine clade A (Thai, Chung & Tran, 2017). The 17,550-years-old sample OWW12 shared the haplotype of several ancient wolves from Alaska, Russia and Czech Republic spanning from 15,000 to 47,000 years old (Stiller et al, 2006; Leonard et al, 2007; Thalmann et al, 2013) and of a modern street dog from Bali (Irion et al, 2005) (see Table 2).…”

“…Currently, the worldwide sequence variants of modern and ancient dogs are split into four main phylogenetic groups (namely A, B, C and D) (Savolainen et al, 1997) and the occurrence of a Late Pleistocene wolf carrying a haplotype belonging to the ancient canine clade A (Thai, Chung & Tran, 2017) could add valuable information on the temporal and spatial origin of haplotypes which could have been one of the “source” wolf population from which dogs originated. Given that, OWW9 could represent one of the oldest specimens with such haplotype.…”

A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs

“…Mitochondrial (MT) sequences were generated by removing indels and variants with quality less than 200 and then applying the remaining variants to the reference sequence using the bcftools consensus. The resulting MT sequences have individually been uploaded to the Canis mtDNA HV1 database (http://chd.vnbiology.com) [48] for haplogroup assignment. The MT analyses workflow used is available at https://github.com/TLenfers/multispecies_mitochondrial_variant_analysis.…”

Sự đa dạng di truyền của chó Bắc Hà dựa vào đoạn trình tự 582bp vùng HV1 trên bộ gen ti thể

“…Các vị trí đa hình được đánh số theo qui chuẩn [18]. Trình tự 582bp vùng HV1 sẽ được định loại haplotype bằng công cụ định loại hpaloytype đã được chuẩn [19]. Các chỉ số đa dạng di truyền như đa dạng haplotype, đa dạng nucleotide được tính toán bằng phần mềm DnaSP v6 [22].…”