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Mol Ecol Resour. 2015 Sep;15(5):1238-42. doi: 10.1111/1755-0998.12386. Epub 2015 Feb 22.

DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals.

Author information

1
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.
2
Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.
3
School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999077, China.
4
Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China.
5
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.
6
Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, M5S 2C6, Canada.

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.

KEYWORDS:

domesticated animal; haplogroup tree; mtDNA; phylogeny; software

PMID:
25655564
DOI:
10.1111/1755-0998.12386
[Indexed for MEDLINE]

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