title: Mitochondrial genomes of domestic animals need scrutiny.
abstract: More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives, as well. Nevertheless, few efforts have been performed to evaluate the sequence data quality. Herein, we conducted a phylogenetic survey of these complete or near-complete mtDNA sequences based on mtDNA haplogroup trees for the eight animals. We show that errors due to artificial recombination, surplus of mutations and phantom mutations do exist in 14.5% (194/1342) of mtDNA sequences and all of them should be treated with wide caution. We propose some caveats for future mtDNA studies of domestic animals.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, 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.forename: Ni-Ni
authors.initials: NN
authors.lastname: Shi
authors.forename: Long
authors.initials: L
authors.lastname: Fan
authors.forename: Yong-Gang
authors.initials: YG
authors.lastname: Yao
authors.forename: Min-Sheng
authors.initials: MS
authors.lastname: Peng
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Zhang
mesh_terms: D000818:Animals; D000829:Animals, Domestic / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D054629:Genome, Mitochondrial; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: data quality; domestic animal; haplogroup; mtDNA; phylogeny