Human Chimp Genome Similarity

[glipsnort (Steve Schaffner)]

@RichardBuggs

I was hoping you might in particular have a chance to respond to this post (especially part b) when you have time:

Okay. . .

@RichardBuggs

The main chimp genome paper did not quantify differences due to structural variation. These were examined in 2005 in a separate paper here, where the authors concluded: “Nevertheless, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species than single-base-pair substitution (1.2%).” So the challenge for me is to explain why this figure now seems to be 5% rather than 2.7%.

I hesitate to conclude that it is now 5%. The MUMmer4 paper concluded that 4% of the chimpanzee genome did not align against the human, which looks quite consistent with the sum of 2.7% from segmental duplications and 1.5% from smaller indels (from the original chimp paper). Aligning the human against chimpanzee of course gives a smaller aligned fraction, but that’s inevitable when aligning the more complete against the less complete genome. (Now, the reciprocal LASTZ alignments may give a different value, but that kind of dependence on method would make any conclusions quite tenuous.)

@RichardBuggs

I am not sure I can agree with you on this point. The authors responsible for this section do not say that these parts of the assembly were wrong.

True.

@RichardBuggs

Their aim seems to be to come up with a higher-level scaffolding of the chimpanzee genome using one-to-one reciprocal best alignments with the human genome. The parts of the chimpanzee assembly that they don’t include in this are copy number variants, scaffolds that align partly to one human chromosome and partly to another, and a few other categories. The authors don’t seem to be suggesting that these were misassembled in the chimpanzee assembly - it is just that they don’t fit in well with an approach to super-scaffolding that assumes that the human and chimpanzee genomes contain no structural rearrangements.

Give their stated doubt that they could assemble structural arrangements correctly, I think they are eliminating a class of alignment that includes incorrect assembly as well as portions of the genome that they don’t think they can assemble correctly. That is not exactly what I said previously.