Lesson 9 Flashcards
Genome
the complete set of genes or genetic material present in a cell or organism
Evolution
change in the heritable characteristics of biological populations over successive generations.
Genomics
- key challenge of modern evolutionary biology
- comparing genomes of different species
- genomes also contain the history of life or evolutionary lineage
Doug langur
Gene duplication allowing it to ferment and digest leaves
Link DNA changes to phenotype
- the key challenge of modern evolutionary biologists- link DNA sequences with the evolution of the complex morphological characters used to construct a traditional phylogeny
- pine trees have~6 times more DNA than humans?!! single-celled amoeba can up to 400 times more!
Most traits are polygenic
As we sequence more genomes, we can compare genomic level differences and
- understand the workings of evolution
- improve crops
- identify the genetic basis of disease
sequenced genomes
- the size of its genome, measured either by DNA content or the number of genes
- Multi-cellular organisms with multiple tissues generally have more genes than eukaryotes without distinct tissues.
Phylogenetic trees
- displays relationships among modern life forms
- ## the relationship between similar organisms, better to focus on more neutral mutations
Human and pufferfish genomes comparison
- common ancestor 450 MYA
- 25% human genes have no counterparts in fugu
- genome rearrangements since mammal lineage and fish diverged
- human genome 50% repetitive DNA but less than 1/6 of fugu sequence repetitive
comparison between human and mouse genome
- diverged about 75 MYA
- a human has 400 million more nucleotides than the mouse
- both have 20,00 genes and they share 99%
- 300 genes unique to either organism(1%)
comparison between human and chimpanzee genomes
- diverged 4.1 MYA
- 1.5% difference in insertions and deletions
- 53 of human-specific indwells lead to loss of function changes- may be loss of hair or larger cranium
- 2.7% of the two genomes have consistent differences in single nucleotides
genomes evolve at different rates
- bacterial evolve in a matter of days
- insects evolve more rapidly than mammalian
- Plants change more rapidly than animal genomes, especially in noncoding DNA
- transposable elements frequently remodel plant genomes.
5% of the human genome contains………….
highly conserved regions of the genome but not ask of the genome, but not all of this is coding
compare plants with animals and fungi
- 1/3 of arabidopsis and Oryza(rice) are plant genes- not found in fungi or animals
genes for photosynthesis and photosynthetic anatomy - the rest are more universal
genes for basic metabolism, genome replication and repair, protein synthesis
how do genes/genomes evolve
- both genome size and gene number vary greatly among the eukaryotes species- contributing factor is whole genome duplication, which results in polyploidy
- occurs commonly in plants
whole genome duplication
- polyploidy(three or more chromosome sets) common in plants:
- autopolyploids- genome duplication within a single lineage(same species)
- allopolyploids- of two lineage followed by genome duplication
-measuring allopolyploidy
Two avenues of research into genome alterations following polyploidization
- Paleopolyploids: studies ancient polyploids to reconstruct history
- Sequence divergence between homologues
- Presence or absence of duplicated gene pairs from hybridization
- Synthetic polyploids (another way to study genome structure)
- Crossing plants most closely related to ancestral species and chemically (colchicine) inducing chromosome doubling
- Without doubling the plant will be sterile because it lacks homologous chromosomes needed to pair during metaphase
- Commercial bananas are 3n and sterile – seedless – aborted ovules appear as brown dots in center of cross section
Polyploidy in plants
- Occurred numerous times in flowering plants
- Polyploidy may provide increased variation and genes for selection to work for
Polyploidy in plants
Expect genomes to continue growing in size after duplication
* But this is not always the case
Polyploidy in plants
- Comparison of soybean, forage legume, and garden pea shows a huge difference in genome size
- Some genomes increased in size through polyploidization
- Some decreased in size through loss of genes or whole chromosomes
Polyploidy in plants
Often, many genes are immediately lost after polyploid event maybe to reduce redundancy
* This may explain the disconnect between genome size and number of genes, and complex
Transposons mobilized by polyploidization
Transposable (mobile) genetic elements Barbara McClintock (Nobel Prize)
* Hypothesized that they are controlling elements, move around the genome, disrupting genes, or rearranging exons
* Respond to genome shock (polyploidization) and jump into a new position
* New phenotypes could emerge
* Transposable element activity increases after polyploidization event
Polyploidy alone doesn’t explain variation in genome size
All genome size variation is not due to polyploidy
* Humans have 9x the amount of DNA found in the pufferfish genome, but around the same number of genes
* Plants can have a 200-fold difference in genome sizes, but all have between 24,000- 60,000 genes
- Tulips have 170 times more DNA than Arabidopsis
Noncoding DNA inflates genome size
Much of the extra DNA in humans compared with pufferfish is in introns
* Large expanses of retrotransposon DNA contribute to difference in genome size
* Both rice and maize have 40,000 protein-coding genes; Rice genome is 370 Mb, maize genome is 2 Gb
– Maize contains lots of repetitive DNA
Polyploidy is change in
the whole set of chromosomes
Aneuploidy is
numerical change in part of the chromosome set
Evolution within genomes
Duplication within parts of the genome can also lead to evolution
* Aneuploidy
– Duplication or loss of an individual chromosome
* Duplication of segments of DNA is one of the greatest sources of novel traits
– Paralogues – two genes within an organism that have arisen from a gene duplication event
– Orthologues – reflects conservation of a single gene from a common ancestor
DNA sequences can be duplicated
Gene families grow through gene duplication Fates of duplicate gene:
– Losing function through subsequent mutation * Fate of most duplicated genes
– Gaining a novel function through subsequent mutation
– Having total function partitioned into the two duplicates
Segment duplication
5% of human genome consists of segmental duplications
Gene duplication in humans
– Most likely to occur in three most gene-rich chromosomes
– Least amount of duplication in seven chromosomes with the least genes
Certain types of human genes more likely to be duplicated
– Growth and development genes, immune system genes, and cell-surface receptors
DNA segments can be rearranged
Humans have 1 fewer chromosome than chimpanzees, gorillas, and orangutans
* Fusion of two chromosomes into one chromosome; chromosome 2 in humans
- phylogenies from the rearrangements
– But how do we re-construct past genome
structural changes
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Conservation of synteny (conservation of large blocks of DNA)
Preservation over evolutionary time of arrangements of DNA segments in related species
* But rearrangements can occur at different rates between species, adding to the complexity of genome size and gene number
– Allows researchers to locate a gene in a different species using information about synteny (Identify markers traveling together)
Rearranged DNA can acquire new functions or lose it
- Loss of Olfactory Receptor genes (pseudogenes)
– Olfactory receptor (OR) genes - Inactivation best explanation for our reduced sense of smell
- 63% of human OR genes are pseudogenes
– Genes that do not produce a functional product due to premature stop codons, missense mutations, or deletions
Rearranged DNA can acquire new functions or lose it
Icefish survive in Antarctic waters due to antifreeze protein
- 9 bp of a gene coding for a digestive enzyme evolved to encode part of an antifreeze protein
- Series of errors persisted only because it coincided with massive cooling of Antarctic water
- Natural selection worked on the chance mutation
Gene swapping and genome
evolution
Horizontal Gene Transfer (HGT)
– Genes hitch hike from other species Contrast to Vertical Gene Transfer (VGT)
– Genes Pass from generation to generation Base of the tree of life is a web rather than a branch
Noncoding DNA
All these rearrangements lead to noncoding-DNA (ncDNA), which makes up much of the genome
* There is also retrotransposon DNA
– 30%ofanimaland40–80%ofplantgenomes
* Much of noncoding DNA is involved with gene regulation – Mayexplainmanydifferencesbetweenspecies
Gene Function and Expression
Patterns
Inferred by comparing genes in different species at different times
– Genes are expressed at different times
– In different tissues
– In different amounts
– In different combinations
* Humans and chimps diverged from a common ancestor only about 4.1 MYA
Chimp DNA is 98.7% identical to human
– Comparing only protein encoding genes it is 99.2% identical
* Differences may be explained by different patterns of gene transcription activity – brain cells
Complex gene expression
- Speech is uniquely human
– Single point mutation in FOXP2 gene means impaired speech and grammar but not in language comprehension
– FOXP2 found in chimps, gorillas, orangutans, rhesus macaques, and mice, yet they don’t speak - Gene expressed in areas of brain that affect motor function
– FOXP2 protein in mice and humans differs by only 3 AA; 2 AA in other primates
Applying Comparative Genomics
Comparative genomics reveals genetic basis for disease
Genome comparisons between pathogen and host aid drug development
Comparative genomics helps conservation biologists
Pathogen-host genome differences reveal drug targets
Malaria caused by protist Plasmodium falciparum with the mosquito Anopheles gambiae as a vector; ~ 1.7– 2.5 million deaths/year
* Plasmodium has apicoplast (non-photosynthetic plastid) where 12% of all its proteins act to produce fatty acids
* Drugs targeted at fatty acid pathway may be effective against malaria
Pathogen-host genome differences reveal drug targets
Amino acids critical to protein function tend to be preserved over the course of evolution, and changes at such sites within genes are more likely to cause disease
Genome comparisons inform conservation biology
Conservation biology
– Tasmanian devil facial tumor disease
– Sequencing of devil genomes showed low genetic diversity, explaining high spread of disease
Comparisons of mitochondrial genomes reveal genetic diversity in organisms
* Polar bears evolved about 150,000 years ago. Geneticists were shocked to find that the entire maternal line of polar bears can be traced back to a brown bear living in Ireland between 20,000 and 50,000 years ago.
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