Genomics in molecular ecology and evolution

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Genomics in molecular ecology and evolution
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GenomicsWhat is it?

• Use of entire DNA sequence to study an organism

What can genomics tell us?

• Evolutionary history of individual genes in the
  genome (Not always the same as the history
  of the genome)
• Clues about metabolic/physioligic capabilites
  based on gene presence or absence

What cant genomics tell us?

• Function of all the genes in the genome
• When they are expressed
• How they interact with one another

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GenomesWhat do they look like?
Prokaryotes

• Often a single circular genome
• Sometimes multiple genomes and/or large plasmids
• A few examples of linear genomes

Eukaryotes

• Diploid2 copies of each chromosome
• Multiple different chromosomes

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GenomesHow Big?
Genome Size of GenesH.
influenzae 1.8 Mb 1700E. coli 4.7
Mb 4400Yeast 12 Mb 6300Fruit Fly 180
Mb 13,600Human 3000 Mb 30,000
1 Mb 1 million base pairs
Source-Oak Ridge National Lab Computational
Genomics Group
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Eukaryotes have a lot of junk DNA
Why isnt there a direct relationship between
genome size and gene content?
Mammalian cellsless than 1 of genomic DNA is
coding
Intron 1
DNA (ds)
Exon 1
Exon 2
Exon 3
Intron 2
transcription
nuclear RNA (ss)
splicing
mRNA (ss) for 1 gene
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Prokaryotes
--much more compact genome structure up to 90
coding
Gene1
Gene 2
Gene 3
DNA (ds)
--much less repetitive DNA
So, genome sequencing started with prokaryotes
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First complete genome sequence of a free-living
organism
1995 Haemophilus influenzae
1,830,137 base pairs (1.8 Mbp), 1743 genes
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How do you sequence an entire genome?
clone library
genomic DNA
sheared to 3kb
insert ends sequenced to 8X coverage
computer assembly of sequence reads
finishing and closure using PCR to close gaps and
verify assembly
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Since 1995 there has been an explosion in the
number of completed genomes
Bacteria 106 completed, 319 ongoing Archaea 16
Completed, 23 ongoing Eukaryotes 19 completed,
235 ongoing
Why? Advances in sequencing technologymajor
sequencing centers have enough capacity to
complete a bacterial genome in a day!
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Case study Escherichia coli
What can we learn from whole genome sequences?

• One of hundreds of microbial species that reside
  in the mammalian colon
• Often used in water quality studies as an
  indicator of fecal contamination
• There are over 170 serogroups of E. coli, the
  majority are not harmful
• BUT..

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Case study Escherichia coli

• One particular type of E. coli called O157 H7 is
  pathogenic
• Responsible for numerous incidents of food
  poisoning in the early 90s
• Many linked to contaminated ground beef
• 1993 outbreak in Seattleover 400 people
  affected, 3 deaths

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What makes O157 H7 different from other E. coli
?
Perna et al., 2001
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O157 H7 contains many more genes

• 1.34 Mbp of DNA
• 1387 additional genes

• 3574 shared genes
• 911 identical proteins

BUT
Relationship between the two strains would be
hard to resolve using a single molecular marker
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Where did the extra genes come from?
Bacterial divide by asexual, clonal
reproduction
Point mutations could arise in the course of DNA
replication
But entire new genses must be acquired from other
organisms 3 mechanisms for this phage plasmi
ds conjugation
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Horizontal (lateral) gene transfer explains the
E. coli strain differences
Eisen, Nature 2001
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A significant fraction of many microbial genomes
may have been acquired through horizontal transfer
Ochman et al., 1999
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What does this mean for microbial evolution?

• New traits are acquired in discrete jumps, rather
  than gradual modification of existing abilities
• Newly acquired capabilities may allow recipient
  to outcompete relatives without additional genes
  and/or colonize new environments
• Examples of horizontally transferred genes
• Virulence factors
• Antibiotic resistance
• Metabolic properties

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So, why arent genomes continually growing in
size?

• Gene Loss
• DNA is expensive to maintain
• Genes (both in the ancestral genome and newly
  acquired) must provide a meaningful function
  (enhance fitness) or they will be lost

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Loss of genes for NO3 and NO2 utilization in
surface dwelling phytoplankton
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What are the genes doing?

• Function is assigned based on degree of
  similarity of an already characterized gene in
  the database
• 2 potential problems with this approach

Transitive catastrophe
Gene A Assigned function based on mutant
phenotype or biochemical characterization of
protein product
Gene B From genome sequence 70 identity to gene
A
Gene C From genome sequence 60 identity to gene
B
Gene D From genome sequence 70 identity to gene
C
But--Gene D has only 20 identity to gene A!
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What if there is nothing at all similar in the
database?
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4
2
20

• Call it a hypothetical gene
• If it has a match but that is to another
  hypothetical gene?
• conserved hypothetical

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4
1
32
2
1
Conserved Hypothetical
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Hypothetical
1
4
DNA Replication Repair
Energy Metabolism
Nucleotide Metabolism
Lipid Metabolism
Transcription
Amino Acid Metabolism
Translation
Carbohydrate Metabolism
Transport
Cofactor Metabolism
Unassigned
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What about eukaryotes?

• Most complete genomes are of model organisms
  (yeast, mustard plant, fruit fly, worm)
• Japanese puffer fish (Fugu rubripes) has smallest
  known vertebrate genome (400 Mb)
• Has helped in predicting 1000 previously
  unrecognized genes in the human genome

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What about eukaryotes?

• Many more organisms in the pipelinealgae,
  insects, birds, sea urchin, sand crab, tilapia,
  zebrafish, atlantic salmon
• Plans to sequence a complete mitochondrial
  genomes in each of the 146 families of mammals

The frozen zoo at the San Diego Zoo
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Key Points

• Genomics technology is advancing rapidly
• Enough data to do comparative evolutionary
  studies in microbes
• Population genomics coming soon
• Genomes are dynamic entities
• Horizontal gene transfer plays an important role
  in evolution
• Gene loss occurs constantly in the environment
• Genomic analyses cannot tell us everything
• A high percentage of genes are of unknown
  function
• Even those genes assigned a function need
  laboratory verification