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 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. Comparative Genomics

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7 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 1/6 th Fugu genome sequence.

8 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. Comparative Genomics

9 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.

10 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. Comparative Genomics

11 Comparison of plants with animals and fungi: –1/3 rd 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 Comparative Genomics

12 Evolution of Whole Genomes Polyploidy can 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)

13 Evolution of Whole Genomes

14 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. Evolution of Whole Genomes

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

16 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. Evolution Within Genomes duplicationloss

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

18 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. Evolution Within Genomes

19 Drosophila –31 new duplicates per genome per million years ( 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. Evolution Within Genomes

20 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. Evolution Within Genomes

21 Chromosomal rearrangement Evolution Within Genomes

22 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. Evolution Within Genomes

23 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 Evolution Within Genomes

24 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. Gene Function and Expression Patterns

25 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.

26 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.