First Draft of Chimpanzee Genome Published September, 2005 3.5X coverage Comparisons to human genome Base pair level Duplications Deletions Evidence of selective pressures In September of 2005, the draft sequence of the genome of the common chimpanzee (Pan trogdolytes) was published in the journal Nature. Though coverage was only 3.5X, it was sufficient to allow researchers to perform a number of key comparisons with the human genome. Base-pair differences and variations in segmental duplications and deletions were closely examined. By comparing the ratio of non-synonymous to synonymous base-pair substitutions in the coding regions of the genes of the two species, researchers were also able to establish evidence for selection in different genes. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

Base pair comparisons Divergence of 1.23% Reprinted by permission from Macmillan Publishers Ltd: Nature, (437: 69-87) From Figure 1 in The Chimpanzee Sequencing and Analysis Consortium “Initial sequence of the chimpanzee genome and comparison with the human genome” (2005). Divergence of 1.23% Agrees with other recent studies Lowest divergence in X-chromosome Highest divergence in Y-chromosome Approximately 2.4 gigabases of sequence from humans and chimpanzees was aligned and used to determine the base-pair divergence between the two species. The results showed a mean divergence rate of 1.23%, which is consistent with other recent studies based on smaller sequence samples. A histogram showing the number of 1 Mb segments with a particular rate of base-pair divergence is shown in the shown in the upper left portion of the slide. Areas shaded in blue represent autosomal sequences. Sequence comparisons for the X- and Y-chromosomes are shown in red and green respectively. The graph in the lower left corner shows the mean level of base-pair divergence and associated error bars for each of the chromosomes. Note that the X-chromosome appears to have the lowest level of divergence, while the Y-chromosome has the most. The greater level of divergence in Y-chromosome sequence is attributable to the higher mutation rate due to the greater number of cell-divisions undergone by male germ cells when compared to the female. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

Segmental differences Magnitude of differences in genomes Due to base-pair divergence: 1.2% Due to indels: 3.0% Due to segmental duplications: 2.7% Duplicated complete and partial genes 177 found in human, but not chimpanzee 94 found in chimpanzee, but not human Duplication rate since divergence 4-5 megabases per million years Base pair comparisons capture only one type of sequence divergence between species. Insertions and deletions (indels) and segmental duplications, where large pieces of DNA, including genes, are duplicated account for a great deal of genomic variation as well. In the case of the human and the chimpanzee, indels and segmental duplications account for 3.0% and 2.7% of the sequence divergence respectively. Differences in indels are mostly due to repeated sequences (greater than one third) and transposable elements (roughly one quarter). An examination of transposable elements shows 7,000 Alu elements in the human genome, but only 2,300 in the chimpanzee’s, indicating that Alu elements have been significantly more active in the human since the lineages of humans and chimpanzees split. In contrast, L1 elements appear to have been equally active in the two species. A study of segmental duplications showed that humans and chimpanzees have a duplication rate of 4-5 megabases per million years. Some of these duplications are shared in the two species, but others appear in one but not the other. A closer look at the coding regions of these duplicated segments showed that 177 complete and partial genes were found in human-only duplications and 94 complete and partial genes were found in chimpanzee-only duplications. Interestingly, some of these species-specific duplicated areas contained genes implicated in various diseases, including Huntington’s disease. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

Evidence of selection Estimating the level of positive selection Examine coding regions KA: rate of non-synonymous substitutions KI: rate of synonymous substitutions Low KA/KI Strong selective constraints High KA/KI Weak selective constraints Evidence for positive selection Highest KA/KI genes Involved in reproduction and immunity The ratio of non-synonymous to synonymous nucleotide substitutions is often used as a measure of selective constraint on a gene. Non-synonymous substitutions lead to a change in the amino acid composition of a protein, while synonymous substitutions have no impact on amino composition at all. By comparing the nucleotide composition of genes between two species, it is possible to measure the level of selective constraint for individual genes. The rate of non-synonymous substitutions is typically represented by KA and the rate of synonymous substitutions is represented by KI. If the ratio of KA to KI is very low, this indicates that a gene is subject to very strong selective constraints, and that even a very small number of amino acid changes will have very negative results for the organisms. Such genes are usually assumed not to be under positive selection. In contrast, when a gene has a KA/KI value greater than one (or near one), this is often (but not always) an indication that a gene is under positive selection. An analysis of homologous genes in the human and chimpanzee genomes yielded an average KA/KI value of 0.23, which is substantially lower than previous estimates based on smaller sets of genes from humans and chimpanzees. However, a subset of 585 genes did show high KA/KI values. Those with the highest values appear to be involved in the reproductive and immune systems. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

Primate genomes on the horizon Gorilla Sequencing begun in October, 2005 Orangutan Draft sequence expected in 2006 Gibbon (lesser ape) Some sequencing planned Rhesus monkey (old world monkey) Due soon Marmoset While comparisons between the human and chimpanzee genomes can tell a great deal about what distinguishes humans from their closest ape relatives, the power of such comparisons is also limited. For example, a segment of DNA that is present in the human, but missing in the chimpanzee doesn’t necessarily indicate a uniquely human sequence. If this particular sequence is present in all of the other great apes, but missing only in the chimpanzee, it may instead indicate something unique about the chimpanzee. In order to have definite answers to such questions, the genomes of additional great apes, and primates in general, will have to be sequenced. Fortunately, a number of such efforts are presently underway. The sequencing of the gorilla genome has already begun and a draft sequence of the orangutan is expected before the end of 2006. The sequences of more distantly related primates like the marmoset and the medically important rhesus monkey are likewise expected to be completed sometime in 2006. Though a full-scale sequencing project is not yet planned for the gibbon (a lesser ape), some sequencing will be done. Sequencing the gibbon genome is especially important for understanding the basis of the unique cognitive abilities that set all great apes apart from the rest of the primate world. The gibbon is a lesser ape and hence the primate that is most closely related to the great apes. However, the gibbon lacks some of the interesting cognitive abilities shared by the great apes. For example, experiments have suggested that gibbons do not recognize themselves in mirrors, while all great apes do. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458