title: DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals.
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.
authors: 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.
authors: Min-Sheng
authors: MS
authors: Peng
authors: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999077, China.
authors: Long
authors: L
authors: Fan
authors: 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.
authors: Ni-Ni
authors: NN
authors: Shi
authors: Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China.
authors: Tiao
authors: T
authors: Ning
authors: 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.
authors: Yong-Gang
authors: YG
authors: Yao
authors: 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.
authors: Robert W
authors: RW
authors: Murphy
authors: 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.
authors: Wen-Zhi
authors: WZ
authors: Wang
authors: 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.
authors: Ya-Ping
authors: YP
authors: Zhang
mesh_terms: D000818:Animals; D000829:Animals, Domestic / Q000145:classification* / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D010802:Phylogeny; D012984:Software
chemical_list: D004272:DNA, Mitochondrial
keywords: domesticated animal; haplogroup tree; mtDNA; phylogeny; software