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Chapter 27 : Comparing Genomes

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Comparing Genomes, Page 1 of 2

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Abstract:

This chapter provides student activity that introduces the concept of using markers, such as repeated sequences, to compare genomes and discusses the various levels at which genomes can be compared: between genera, species, breeds within a species, or individuals. It contains a paper that provides the foundation for understanding how restriction analysis and polymerase chain reaction (PCR) can be used for genome comparisons and discusses the use of mitochondrial DNA in genetic studies. The information in the student introduction provides a brief overview of how genomes change and what sorts of questions can be addressed with genome comparisons, explains two approaches to DNA typing, and illustrates their use by focusing on the analysis of dog genomes. The activity describes the process for identifying a microsatellite marker. The technique of whole-genome hybridization and the comparison of the appearance of chromosomes in karyotypes were the only methods available for comparing genomes until the 1980s. Some molecular scientists now argue that genetic distance should also be grounds for defining species. The activity uses the dog genome as an example of ways in which genome comparisons and genome typing can be used to answer a variety of questions. It illustrates how PCR or Southern hybridization can be used to distinguish microsatellite alleles.

Citation: Kreuzer H, Massey A. 2008. Comparing Genomes, p 382-400. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch27

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Restriction Fragment Length Polymorphism
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Citation: Kreuzer H, Massey A. 2008. Comparing Genomes, p 382-400. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch27
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Citation: Kreuzer H, Massey A. 2008. Comparing Genomes, p 382-400. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch27
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Figure 27.1

Structural similarities and differences in chromosomes 1 to 3 of primates. H, human; C, chimpanzee; G, gorilla; O, orangutan.

Citation: Kreuzer H, Massey A. 2008. Comparing Genomes, p 382-400. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch27
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Figure 27.2

Variation in the numbers of tandem (head-to-tail) repeat sequences at many different locations within the genome provides a basis for genetic fingerprinting. To generate a fingerprint, laboratory technicians amplify many different loci using a specific set of primers for each one or they digest the sample DNA with restriction enzymes known to cut it at sites flanking the repeats.

Citation: Kreuzer H, Massey A. 2008. Comparing Genomes, p 382-400. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch27
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Citation: Kreuzer H, Massey A. 2008. Comparing Genomes, p 382-400. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch27
Permissions and Reprints Request Permissions
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Citation: Kreuzer H, Massey A. 2008. Comparing Genomes, p 382-400. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch27
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Image of Figure 27.3
Figure 27.3

Human mitochondrial DNA. The D-loop region around the origin of replication is the hypervariable region.

Citation: Kreuzer H, Massey A. 2008. Comparing Genomes, p 382-400. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch27
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Figure 27.4

Inheritance of mitochondrial DNA follows the maternal line.

Citation: Kreuzer H, Massey A. 2008. Comparing Genomes, p 382-400. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch27
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References

/content/book/10.1128/9781555816100.chap27a
1. Ellgren, H. 2005. The dog has its day. Nature 438:745746. A news story/comment about the first publication of a complete dog genome sequence.
2. Jeffreys, A. 2005. DNA fingerprinting. Nature Medicine 11(10): xivxviii. A nontechnical retrospective about the development of DNA fingerprinting by the scientist who introduced it to the world.
3. Morell, V. 1994. Decoding chimp genes and lives. Science 265:11721173. A nontechnical overview of the chimpanzee studies.
4. Morrell, V. 1997. The origin of dogs: running with the wolves. Science 276:16471648. News commentary on the evolutionary study of dog DNA; accompanied the publication of the Science article by Vila et al. listed below.
5. Ostrander, E.,, and R. Wayne. 2005. The canine genome. Genome Research 15:17061716. A review by two of the leaders in dog genome research that summarizes studies of dog evolution, breed diversity and origins, disease gene mapping, and behavioral genetics. This article is available free of charge at http://www.genome.org (all articles published in this journal are free 6 months after the date of publication).
6. Parker, H. G., et al. 2004. Genetic structure of the purebred domestic dog. Science 304:11601164. An original research paper in which microsatellite markers were used to study relationships among 85 dog breeds.
7. Pennisi, E. 2004. Genome resources to boost canines' role in gene hunts. Science 304:10931094. A discussion of how progress in understanding the dog genome and developing molecular tools like microsatellite markers have made purebred dogs an invaluable resource for gene hunters; accompanied the publication of the Science article by Parker et al. listed above.
8. Pollinger, J. P., et al. 2005. Selective sweep mapping of genes with large phenotypic effects. Genome Research 2005 15:18091819. This article describes the study that identified the region of the dachshund genome near the fibroblast growth factor receptor gene as being invariant (see the introduction to the Student Activity). The article is available free of charge at http://www.genome.org.
9. Vila, C., et al. 1997. Multiple and ancient origins of the domestic dog. Science 276:16871689. Original research article describing the evolutionary analysis of dog and wolf mitochondrial DNA.
10. Vila, C.,, J. Maldonado,, and R. Wayne. 1999. Phylogenetic relationships, evolution, and genetic diversity of the domestic dog. Journal of Heredity 90:7177.
11. Cann, R. L.,, and A. C. Wilson. 2003. The recent African genesis of humans. Scientific American 289:5461.
12. King, M.-C. 1990. Genes of war. Discover 11(10):4652. The story of Mary-Claire King's work in Argentina.
13. National Institutes of Health. http://www.nlm.nih.gov/exhibition/visible proofs/galleries/cases/index.html. The story of the identification of Michael Blassie, along with several other cases of forensic interest (including one related to the identification of the children of the Argentine victims), can be found on this website.
14. Wallace, D. C. 1997. Mitochondrial DNA in aging and disease. Scientific American 277:4047.

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