Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals

Arong Luo,Aibing Zhang,Weijun Xu,Weifeng Shi,Simon Yw Ho,Yanzhou Zhang,Stephen L Cameron,Chaodong Zhu

doi:10.1186/1471-2164-12-84

Abstract

BackgroundA well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5' half of the mitochondrial cytochrome oxidase 1 gene (CO1) to diagnose and delimit species. However, there is no compelling a priori reason for the exclusive focus on this region, and it has been shown that it performs poorly for certain animal groups. To explore alternative mitochondrial barcoding regions, we compared the efficacy of the universal CO1 barcoding region with the other mitochondrial protein-coding genes in eutherian mammals. Four criteria were used for this comparison: the number of recovered species, sequence variability within and between species, resolution to taxonomic levels above that of species, and the degree of mutational saturation.ResultsBased on 1,179 mitochondrial genomes of eutherians, we found that the universal CO1 barcoding region is a good representative of mitochondrial genes as a whole because the high species-recovery rate (> 90%) was similar to that of other mitochondrial genes, and there were no significant differences in intra- or interspecific variability among genes. However, an overlap between intra- and interspecific variability was still problematic for all mitochondrial genes. Our results also demonstrated that any choice of mitochondrial gene for DNA barcoding failed to offer significant resolution at higher taxonomic levels.ConclusionsWe suggest that the CO1 barcoding region, the universal DNA barcode, is preferred among the mitochondrial protein-coding genes as a molecular diagnostic at least for eutherian species identification. Nevertheless, DNA barcoding with this marker may still be problematic for certain eutherian taxa and our approach can be used to test potential barcoding loci for such groups.

Highlights

A well-informed choice of genetic locus is central to the efficacy of DNA barcoding
Bos indicus was recovered as a barcode species only in two trees derived from profiles of the cytochrome oxidase 1 gene (CO1) barcoding region and ND4L respectively, and had only one representative sequence in profiles of the ATP6, ATP8, and the whole genome
The two sequences of Ursus arctos almost always formed a paraphyletic group with respect to the monophyletic cluster of Ursus maritimus, both of them were recovered as barcode species in trees derived from the ND4 and ATP8 profiles

Summary

Introduction

A well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5’ half of the mitochondrial cytochrome oxidase 1 gene (CO1) to diagnose and delimit species. One of the issues central to the efficacy of DNA barcoding is the selection of a suitable barcode [17] Interspecific variability in this region should be clearly greater than intraspecific variability, the so-called “barcoding gap"; a threshold value for the magnitude of interspecific variation being 10 times that of intraspecific variation has been proposed as being diagnostic of species-level differences [7,11,17]. MtDNA still offers several advantages compared with nuclear DNA: rapid evolution, limited exposure to recombination, lack of introns, and high copy number These characteristics of mtDNA are important for routine amplification by polymerase chain reaction (PCR) and use as a molecular marker for lower-level questions [7,17,24]

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Results

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Conclusion