TED, February 27-March 1, 2008, Monterey: Anything unheard before?

The human mitochondrial consensus genome sequence by Robert Carter

For historical reasons the standard human mitochondrial sequence, the Revised Cambridge Reference Sequence (rCRS) is a reconstruction of a single European individual’s mtDNA and contains several rare alleles. That’s why many times a usual mtDNA sequence alignment must appeal to phylogenetic historical reconstructions. The rCRS nevertheless provides a uniform nucleotide numbering scheme (0-16569). On the other hand, as there are thousands of high-quality, full-length mitochondrial sequences are now available, Robert Carter thought that it is time to construct and analyze a comprehensive human mitochondrial consensus sequence and published his efforts in Nucleic Acid Research, March, 2007: Mitochondrial diversity within modern human populations The sequence itself available as a supplementary material but with the permission of the author I copy it into this post below.

According to Robert Carter:

So far, all feedback has been good. By introducing the idea of “poly-x” sites (see later), I successfully created a technique that avoids all pre-conceived ideas about genetic history. This also allows one to effectively deal with indels, something that many authors have avoided in the mtDNA literature.

Briefly, 827 sequences were used, a master sequence alignment was created in BioEdit and BioPerl was used for all calculations using the rCRS as a template for nucleotide numbering.