1. The Content of the Genome
Chapter 4
The Content of the Genome

2. 4.1 Introduction
The transcriptome and proteome of a cell are generally smaller than its genome
The transcriptome and proteome of the whole organism are generally larger than its genome.

3. 4.2 Genomes Can Be Mapped at Several Levels of Resolution
Linkage maps are based on the frequency of recombination between genetic markers.
Restriction maps are based on the physical distances between markers.
Molecular characterization of mutations can be used to reconcile linkage maps with physical maps.

4. 4.2 Genomes Can Be Mapped at Several Levels of Resolution
Figure 4.01: Some point mutations change the restriction map.

5. 4.3 Individual Genomes Show Extensive Variation
Polymorphism may be detected:
at the phenotypic level when a sequence affects gene function
at the restriction fragment level when it affects a restriction enzyme target site
at the sequence level by direct analysis of DNA
The alleles of a gene show extensive polymorphism at the sequence level, but many sequence changes do not affect function.

6. 4.3 Individual Genomes Show Extensive Variation
Figure 4.02: Restriction sites show Mendelian inheritance.
Photo courtesy of Ray White, Ernest Gallo Clinic and Research Center, University of California, San Francisco

7. 4.4 RFLPs and SNPs Can Be Used for Genetic Mapping
RFLPs and SNPs can be the basis for linkage maps.
They are useful for establishing parent–offspring relationships.

8. Figure 4.03: RFLPs are genetic markers.

9. 4.4 RFLPs and SNPs Can Be Used for Genetic Mapping
Figure 4.04: RFLPs can be associated with disease genes.

10. 4.5 Why Are Some Genomes So Large?
There is no clear correlation between genome size and genetic complexity.
Figure 4.05: Is DNA content related to morphological complexity?

11. 4.5 Why Are Some Genomes So Large?
There is an increase in the minimum genome size required to make organisms of increasing complexity.
There are wide variations in the genome sizes of organisms within many taxa.

12. 4.5 Why Are Some Genomes So Large?
Figure 4.06: Minimum genome size increases with the taxon.

13. Figure 4.07: Comparison of genome sizes.

14. 4.6 Eukaryotic Genomes Contain Both Nonrepetitive and Repetitive DNA Sequences
The kinetics of DNA reassociation after a genome has been denatured distinguish sequences by their frequency of repetition in the genome.
Polypeptides are generally coded by sequences in nonrepetitive DNA.
Larger genomes within a taxon do not contain more genes, but have large amounts of repetitive DNA.
A large part of moderately repetitive DNA may be made up of transposons.

15. Figure 4.08: Nonrepetitive DNA is only part of the genome.

16. 4.7 Eukaryotic Protein-Coding Genes Can Be Identified by the Conservation of Exons
Conservation of exons can be used as the basis for identifying coding regions by identifying fragments whose sequences are present in multiple organisms.
Human disease genes are identified by mapping and sequencing DNA of patients to find differences from normal DNA that are genetically linked to the disease.

17. Figure 4.09: Genes can be identified by deletions.
4.7 Eukaryotic Protein-Coding Genes Can Be Identified by the Conservation of Exons
Figure 4.09: Genes can be identified by deletions.

18. Figure 4.10: The DMD gene codes for a muscle protein.

19. Figure 4.11: A special vector is used for exton trapping.

20. 4.8 The Conservation of Genome Organization Helps to Identify Genes
Methods for identifying active genes are not perfect and many corrections must be made to preliminary estimates.
Pseudogenes must be distinguished from active genes.
There are extensive syntenic relationships between the mouse and human genomes, and most active genes are in a syntenic region.

21. Figure 4.12: Exons are identified by flanking sequences and ORFs.

22. Figure 4.13: Syntenic blocks vary in length.

23. 4.9 Some Organelles Have DNA
Mitochondria and chloroplasts have genomes that show non-Mendelian inheritance.
Typically they are maternally inherited.
Organelle genomes may undergo somatic segregation in plants.
Comparisons of mitochondrial DNA suggest that it is descended from a single population that lived 200,000 years ago in Africa.

24. 4.9 Some Organelles Have DNA
Figure 4.14: Uneven segregation causes somatic variation.

25. Figure 4.15: Animal mtDNA is inherited from the mother.

26. 4.10 Organelle Genomes Are Circular DNAs That Code for Organelle Proteins
Organelle genomes are usually (but not always) circular molecules of DNA.
Organelle genomes code for some, but not all, of the proteins found in the organelle.

27. 4.10 Organelle Genomes Are Circular DNAs That Code for Organelle Proteins
Animal cell mitochondrial DNA is extremely compact and typically codes for 13 proteins, 2 rRNAs, and 22 tRNAs.
Yeast mitochondrial DNA is 5× longer than animal cell mtDNA because of the presence of long introns.

28. 4.10 Organelle Genomes Are Circular DNAs That Code for Organelle Proteins
Figure 4.16: Mitochondria code for RNAs and proteins.
Figure 4.17: Most human mtDNA is expressed.

29. Figure 4.17: Most human mtDNA is expressed.

30. 4.11 The Chloroplast Genome Codes for Many Proteins and RNAs
Chloroplast genomes vary in size, but are large enough to code for 50 to 100 proteins as well as the rRNAs and tRNAs.
Figure 4.19: Chloroplasts have >100 genes.

31. 4.12 Mitochondria and Chloroplasts Evolved by Endosymbiosis
Both mitochondria and chloroplasts are descended from bacterial ancestors.
Most of the genes of the mitochondrial and chloroplast genomes have been transferred to the nucleus during the organelle’s evolution.

32. 4.12 Mitochondria and Chloroplasts Evolved by Endosymbiosis
Figure 4.20: Endosymbiosis results from cell capture.