Friday, August 11, 2006 - 06:14
During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are. Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck right inside of chromosome 17! The existence of this extra mitochondrial sequence probably complicates some genetic analyses. One of my readers also asked an interesting question about whether apes have a similar mitochondrial sequence in their equivalent of chromosome 17, and how it compares. We will come back to that question, later on. For now, I'm going to return to the original question, and finish our first comparison of human mitochondrial DNA sequences and with the mitochondria from the great apes. To compare human and ape mitochondria, I used the NCBI web server to run blastn and compare a human mitochondrial reference sequence with great ape sequences (see how it's done). Last week, I showed some of the blast results. These results contained a graph illustrating where the ape sequences matched the human sequence. Now, we're going to take this a step further. I went through the blast results, found which parts of the sequences matched each other, and found the number of bases that matched in each region. Then, I added up the number of bases that matched for each mitochondrial sequence and divided by the number of bases in the human mitochondria to calculate the percent of matching bases for the entire mitochondrial genome. I also made a map and put the matching sequences in order to make sure that I didn't count any sections twice. For example, for Pan paniscus (Bonobo chimp), I get something like this: Matching region   number matching 1-239                         223 263-448                         165 525-567                            39 579-16,524                   14,581 total matching bases from the Bonobo chimp = 15,008 bases The human mitochondrial sequence is 16,571 bases in size, so for Pan paniscus, we have: 15,008 bases matching out of 16,571, or 90.6% I'm not doing anything fancy to compensate for gaps or gap distance here, just looking at the percent of matching bases across the mitochondrial genome. For Pan troglodytes(Chimpanzee): 15,0303 bases out of 16,571, or 90.7% And for Gorilla gorilla(Gorilla), we have: 14,448 out of 16,571, or 87.2% Our first question has been answered - at least for the mitochondrial genome. Our mitochondrial DNA is a little over 90 percent similar to that of Bonobo chimps and Chimpanzees and 87% similar to Gorillas. Of course, this isn't the whole story. There's a bit more information here that we can uncover. If, we can compare the mitochondrial DNA from the apes to each other, we can make a graph that shows the relationships between all four of species, Human, Bonobos, Chimps and Gorillas. Here's your assignment for next week: compare the mitochondrial sequences from Bonobos to Chimps and Gorillas, and the mitochondrial sequence from the chimp to the sequence from the Gorilla. Next Friday, we'll use the sequences and construct a simple tree to look at all four relationships.