Human Chimp Genome Similarity

[RichardBuggs]

Hi Steve,

I have quite a backlog of questions to deal with, and only half an hour free, so I will try to tick off one of the major ones.

In response to my comment:

@RichardBuggs

Here are the results I get for reciprocal best alignments with successively better chimpanzee genome assemblies:

hg38 v panTro3 82.3%

hg38 v panTro4 82.3%

hg38 v panTro5 84.2%

hg38 v panTro6 84.4%

I am very happy to share my script for you to check if you want, or perhaps you would prefer to do your own independent analysis.

It would appear that improved chimpanzee assemblies between versions 3 and 6 of the chimpanzee genome have only yielded small decreases to the non-aligned parts of the human genome.

You said

@glipsnort

How much additional sequencing has been done of the chimpanzee genome?

As far as I can make out from NCBI, PanTro 3 and 4 were based on 6x Sanger genome coverage. PanTro5 had an additional 55x coverage of Illumina overlapping paired 250bp length reads, 2 Lanes of a Chicago library (Hi-C from Dovetail Genomics) and 9x coverage of PacBio long single molecule reads. The total sequence length of PanTro5 is 3,231,154,112bp (ungapped length =3,132,603,083bp), whereas PanTro4 is 3,309,561,368 (2,902,353,696bp ungapped).

I think it is worth noting that although PanTro5 has considerably more data that PanTro4, and is 8% longer in its ungapped length, it has only yielded an increase of one-to-one orthology with the human genome of 1.9% (from 82.3% to 84.2%).

I can’t find anything online about PanTro6. If you have access to information about how this is an improvement on PanTro5, I would be very grateful.