Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity

Since the original 2005 report for the chimpanzee (chimp) genome assembly (5X rough draft), an additional one-fold redundant coverage has been added. Using the new 6X chimpanzee assembly, a sequential comparison to the human genome was performed on an individual chromosome basis. The chimpanzee chromosomes, were sliced into new individual query files of varying string lengths and then queried against their human chromosome homolog using the BLASTN algorithm. Using this approach, queries could be optimized for each chromosome irrespective of gene/feature linear order. Non-DNA letters (gap-filling ‘N’s) were stripped from the query data and excluded from the analyses. The definition of similarity for each chromosome was the amount (percent) of optimally aligned chimp DNA. This definition was considered to be conservative because it did not include the amount of human DNA absent in chimp nor did it include chimp DNA that was not aligned to the human genome assembly (unanchored sequence contigs). For the chimp autosomes, the amount of optimally aligned DNA sequence provided similarities between 66 and 76%, depending on the chromosome. In general, the smaller and more gene-dense the chromosomes, the higher the DNA similarity—although there were several notable exceptions defying this trend. Only 69% of the chimpanzee X chromosome was similar to human and only 43% of the Y chromosome. Genome-wide, only 70% of the chimpanzee DNA was similar to human under the most optimal sequenceslice conditions. While, chimpanzees and humans share many localized protein-coding regions of high similarity, the overall extreme discontinuity between the two genomes defies evolutionary timescales and dogmatic presuppositions about a common ancestor.