Comparisons between mitochondrial genomes of domestic goat (Capra hircus) reveal the presence of numts and multiple sequencing errors

Abstract

Materials and methods. In the present study, we amplified and sequenced the complete mitochondrial genome from a Vietnamese domestic goat (Capra hircus). The data were compared with mtDNA sequences available in the nucleotide databases.

Results. The results revealed many problems in the goat mitochondrial reference genome (GenBank accession number NC_005044). Firstly, the authors did not sequence the complete genome, simply 44.5% of its total length. Secondly, two fragments (representing 1201 and 2384 nt) contained an unusually high percentage of sequencing errors. Thirdly, a segment of 1881 nt, covering most of nd5 and the 5′ part of nd6, was shown to be a nuclear sequence of mitochondrial origin (Numt). Surprisingly, a similar Numt was also detected in four other goat mitochondrial genomes available in GenBank (GU22978-81). Two primers were designed specially to amplify ∼960 nt of the Numt identified in goat mtDNA genomes. After cloning, two Numts were detected for C. hircus. Several Numts, most of them with stop codon or frameshift mutations, were also found in Hemitragus jemlahicus (Himalayan tahr) and Pseudois nayaur (bharal). Phylogenetic analyses suggest that a nuclear integration occurred in the common ancestor of Ammotragus, Arabitragus, Capra, Hemitragus and Pseudois, followed by several subsequent duplication events.

Conclusion. As poor-quality sequences can produce misleading interpretations of both phylogeny and molecular evolution, we propose including a new link to each accession number in the nucleotide databases, named “external expertise”, which could be openly and continually updated by non-anonymous searchers in order to validate good-quality data, or, conversely, to indicate possible problems in the sequence, such as DNA contamination or sequencing errors. This information could prove very useful over time to select good-quality sequences for in silico analyses.

Keywords::

• mtDNA genome
• goat
• Capra
• Bovidae
• Caprini
• Numt

Acknowledgements

The authors would like to thank Anne Ropiquet for her helpful comments, Trung Thanh Nguyen for information on Vietnamese goat breeds and Pietro Parma for the bibliography. They also thank the anonymous reviewer and Sergios-Orestis Kolokotronis for useful suggestions.

Declaration of interest: This work was supported by the Muséum national d'Histoire naturelle (MNHN), CNRS, PPF “Etat et structure phylogénétique de la biodiversité actuelle et fossile” and “Consortium National de Recherche en Génomique”. This work is part of Agreement No. 2005/67 between Genoscope and the MNHN on the project “Macrophylogeny of Life”.