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THE TARGET
Target DNA
Although there has
never been a broadly based effort to implement a microgenomic
identification system for animals, enough work has been
done to indicate key design elements. It is clear that
the mitochondrial (mt) genome of animals represents a
better target for analysis than the nuclear genome because
of its lack of introns, its limited exposure to recombination
and its haploid mode of inheritance. As well, there are
robust primers that enable the recovery of specific segments
of the mt genome from a broad range of animals.
Target Gene
Past phylogenetic work has
often focused on mitochondrial genes encoding ribosomal
(12S, 16S) DNA, but their utility in taxonomic analyses
is constrained by the prevalence of insertions and deletions
(indels) that complicate sequence alignments. The 13 protein-coding
genes in the animal mt genome are a better target because
indels are rare since most lead to a shift in the reading
frame. There is no compelling a priori reason
to focus on a specific gene, but the cytochrome c oxidase
I gene (COI) does have two important advantages. Firstly,
the universal primers for this gene are very robust, enabling
recovery of its 5' end from the representatives of most,
if not all, animal phyla. As well, COI likely possesses
a greater range in phylogenetic signal than any other
mitochondrial gene. In common with other protein-coding
genes, its third position nucleotides show a high incidence
of base substitutions. However, changes in its amino acid
sequence occur more slowly than those in any other mitochondrial
gene.
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