Transcript Document

Genome Evolution
Chapter 24
1
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.
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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.
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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.
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Comparative Genomics
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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 1/6th
Fugu genome sequence.
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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.
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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.
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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.
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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
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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)
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Evolution of Whole Genomes
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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.
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Evolution of Whole Genomes
Polyploidy may be followed
by the unequal loss of
duplicate genes from the
combined genomes.
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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
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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.
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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.
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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.
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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.
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Evolution Within Genomes
Chromosomal rearrangement
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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.
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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
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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.
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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.
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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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