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Genome Evolution Chapter 24

Genome Evolution Chapter 24. Introduction. Genomes contain the raw material for evolution; Comparing whole genomes enhances Our ability to understand evolution; To improve crops; To identify genetic basis of disease. Comparative Genomics.

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Genome Evolution Chapter 24

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  1. Genome Evolution Chapter 24

  2. Introduction • Genomes contain the raw material for evolution; • Comparing whole genomes enhances • Our ability to understand evolution; • To improve crops; • To identify genetic basis of disease.

  3. Comparative Genomics • Making the connection between a specific change in a gene and a modification in a morphological character is difficult; • Genomes carry information on the history of life; • Evolutionary differences accumulate over long periods.

  4. Comparative Genomics • Genomes of viruses and bacteria evolve in a matter of days; • Complex eukaryotic species evolve over millions of years; • Example: tiger pufferfish (Fugu rubripes), mouse (Mus musculus), and human genomes.

  5. Comparative Genomics

  6. Comparative Genomics • Comparison between human and pufferfish genomes: • Last shared common ancestor 450 MYA; • 25% human genes no counterparts in Fugu; • Extensive genome rearrangements since mammal lineage and teleost fish diverged; • Human genome is 97% repetitive DNA; • Repetitive DNA less than 1/6thFugu genome sequence.

  7. Comparative Genomics • Human and mouse genomes: • Human: 400 million more nucleotides than the mouse; • 25,000 genes and they share 99%; • Diverged about 75 MYA; • 300 genes unique to either organism (1%); • Rearrangements of chromosomal regions large and small.

  8. Comparative Genomics • Human and chimpanzee genomes: • Diverged 35 MYA; • 1.06% of the two genomes have fixed differences in single nucleotides; • 1.5% difference in insertions and deletions; • 53 of human-specific indels lead to loss-of-function changes; • Smaller ratio in nonsynonymous to synonymous changes; • Purifying selection: removal of nonsynonymous genes.

  9. Comparative Genomics • Genomes evolve at different rates; • Mouse DNA has mutated twice as fast as human; • Fruit fly and mosquito evolve more rapidly than vertebrates; • Difference in generation time accounts for different rates of genome evolution.

  10. Comparative Genomics Comparison of plants with animals and fungi: • 1/3rd genes in Arabidopsis and rice “plant” genes: distinguish plant kingdom from animal kingdom; • Remaining genes similar to genes found in animal and fungal genomes: • Basic intermediary metabolism • Genome replication and repair • RNA transcription & protein synthesis

  11. Evolution of Whole Genomes • Polyploidycan result from: • Genome duplication in one species • Hybridization of two different species • Autopolyploids: genome of one species is duplicated through a meiotic error • Four copies of each chromosome • Allopolyploids: result from hybridization and duplication of the genomes of two different species (tobacco)

  12. Evolution of Whole Genomes

  13. Evolution of Whole Genomes • Plant polyploidy is ubiquitous, with multiple common origins; • Comparison of soybean, forage legume, and garden pea shows a huge difference in genome size; • Some genomes increased, some decreased in size; • Polyploidy induces elimination of duplicated genes.

  14. Evolution of Whole Genomes Polyploidy may be followed by the unequal loss of duplicate genes from the combined genomes.

  15. Evolution Within Genomes • Aneuploidy: duplication or loss of an individual chromosome; • Plants are able to tolerate aneuploidy better than animals; • Duplication of segments of DNA is one of the greatest sources of novel traits. duplication loss

  16. Evolution Within Genomes • Fates of duplicate gene: • Losing function through mutation; • Gaining a novel function through mutation; • Having total function partitioned into the two duplicates.

  17. Evolution Within Genomes • Gene duplication in humans is most likely to occur in three most gene-rich chromosomes: Growth and development genes;Immune system genes;Cell-surface receptor genes; • 5% of human genome consists of segmental duplications; • Duplicated genes have different patterns of gene expression; • Rates of duplication vary for different groups of organisms.

  18. Evolution Within Genomes • Drosophila • 31 new duplicates per genome per million years (0.0023 duplications per gene per million years); • C. elegans 10 times fast rate. • Paralogues: two genes within an organism that have arisen from duplication of a single gene in an ancestor. • Orthologues: conservation of a single gene from a common ancestor.

  19. Evolution Within Genomes Genome reorganization • Humans have 1 fewer chromosome than chimpanzees, gorillas, and orangutans; • Fusion of two genes into one gene; chromosome 2 in humans; • Chromosomal rearrangements in mouse ancestors have occurred at twice the rate seen in humans.

  20. Evolution Within Genomes Chromosomal rearrangement

  21. Evolution Within Genomes Variation in genomes: • Conservation of synteny: the preservation over evolutionary time of arrangements of DNA segments in related species: • Long segments of chromosomes in mice and humans are the same; • Allows researchers to locate a gene in a different species using information about synteny.

  22. Evolution Within Genomes Gene inactivation results in pseudogenes: • Loss of gene function: way for genomes to evolve • Olfactory receptor (OR) genes: inactivation best explanation for our reduced sense of smell • Primate genomes: > 1000 copies of OR genes; • Pseudogenes: sequences of DNA that are similar to functional genes but do not function • 70% of human OR genes are inactive pseudogenes • >50% gorilla & chimpanzee OR genes function • >95% New World monkey OR genes work well

  23. Gene Function and Expression Patterns • Inferred by comparing genes in different species; • Why a mouse develops into a mouse and not a human: • Genes are expressed at different times; • In different tissues; • In different amounts; • In different combinations; • Example: cystic fibrosis gene.

  24. Gene Pattern and Expression • Diverse life forms emerge from similar toolkits of genes; • To understand functional difference: • Look at time and place of expression; • Small changes in a protein can affect gene function.

  25. Genome Size and Gene Number • Genome size has varied over evolutionary time; • Increases or decreases in size do not correlate with number of genes; • Polyploidy in plants does not by itself explain differences in genome size; • A greater amount of DNA is explained by the presence of introns and nonprotein-coding sequences than gene duplicates.

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