Vertebrate Mitochondrial Genome Assessment

First, we created a reference database representative of the mitochondrial genomes of all vertebrates, by retrieving from Genbank all the complete mitochondrial genomes of Vertebrates available (accession: September 2007). Subsequently, we randomly selected one sequence per species, to reduce the overrepresentation of a few species (e.g., humans, mouse, zebrafish etc.). We obtained a set of 814 mitochondrial genomes representative of the five major monophyletic clades of vertebrates [Chondrichthyes: 8 species; Actinopterigii: 385 species; Amphibia: 79 species; Sauropsida (= birds + "reptiles"): 133 species; Mammalia: 202 species; other taxa: 7 species]. Most of species were the unique representative of their genus and the database corresponded to 633 genera.
To analyze the performance of each primer pair studied, we first performed an in silico PCR on the reference database and we evaluated the taxonomic coverage of each primer pair as the proportion of amplified taxa. Then, we performed an in silico PCR on the whole GenBank, to evaluate the resolution of the amplified fragments that represents the proportion of unambiguously identified taxa. These properties were evaluated for the whole Vertebrates and for each of the five clades which compose it.