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Genomics

Martin Polzmpolz@mit.edu

Overview

I. Genome sizesII. How to sequence entire genomesIII. Genome evolution

1. Point mutations2. Regional changes3. Global changes

IV. Environmental genomics

I. Genome sizes Bacterial genome: 6×105 to more than 107

Smallest known: Mycoplasma genitalium (480 protein coding genes, 3 rRNA genes,33 tRNA genes)

Prokaryotes genome sizes are roughly proportional to gene numbers.

Eukayotic genome: 8.8×106~ 6.9×1011

Smallest known include: Saccharomyces cerevisiae and other fungi

Eukaryotes genome sizes are NOT proportional to gene numbers oranatomical complexity

12670,000,000,000Amoeba dubia

233,454,200,000Human

6900,000,000Housefly

12655,000,000Tomato

391,200,000,000Chicken

2090,000,000,000Trumpet lily

Chromosome number (n)Genome size (bp)

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Fungi

Microsp

oridian

s

Animals

Amoebae

Slime m

olds

Land plan

ts

Apicomplex

a

Kinetoplas

tids

Diplomonads

Archea

oglobus

Methan

ococc

us

Methan

obacter

ium

Sulfolobus

Flavobac

teria

Cyanobac

teria

Purple bac

teria

Green su

lfur b

acter

ia

Gram-posit

ive bac

teria

Thermotoga

Aquifex

BACTERIA ARCHAEA EUKARYA

II. How can we sequence entire genomes? Chapter 16

BAClibrary

GenomicDNA

SEQUENCING A GENOME1. Cut DNA intofragments of ~160 kb,using different restrictionsenzymes.

2. Insert fragmentsinto bacterial artificialchromosomes, grow inE. coli cells.

3. Analyze fragments,locate each on map ofgenome.

Figure 16.3 upper

“Shotgunclones”

4. Cut each 160 kbfragment into 1 kbfragments.

5. Insert 1 kb fragmentsinto plasmids, grow inE.coli cells.

6. Sequence eachfragment (note thatends of fragmentsoverlap).

Shotgun sequence

TAGACTCGATAAGGATGC......ATTTAGACTCGATAA

Figure 16.3 middle

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Draft sequence 8. Assemble fragmentsfrom different BACs bymatching overlappingends.

7. Assemble 1 kbfragments fromwithin each 160 kbfragment bymatchingoverlapping ends.

...ATTTAGACTCGATAAGGATGC...

Figure 16.3 lower

Open reading frame (ORF)

StopStart

Figure 16.4

5’ …C T C A A T G G G T A C G T A G G AT C G G G A A T C G T A C A G G A A C G T T T G A A A T C G... 3’ … G A G T T A C C C A T G C A T C C T A G C CC T T A G C A T G T C C T T G C A A A C T T T A G C...

Genome mapIII. Genome evolution

1. Point mutations- measure evolutionary relationships(phylogeny) --> see last lecture

2. “Regional” change- duplication- deletion- mobile elements- chromosome rearrangements

3. “Global” change- genome duplication --> not covered

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Mechanisms of gene deletion or duplication

unequal crossing over replication errors

Consequences of gene duplication

- part of a gene:if functional domain is duplicated --> functional enhancement

-complete genegene dosage enhancedNew function can evolve due to relaxed selection on one copy

1 2 3 4 5 65’ 3’

Ancestral trypsinogengene

1 6’5’ 3’

Thr Ala Ala Gly

1 6’5’ 3’

Deletion

4 fold duplication + addition of spacer sequence

Internal duplications + addition of intron sequence

15’ 1 2 3 4 5 6 7 37 38 39 40 41 3’6’…

Antifreeze glycoprotein gene

Spacer: Gly

Example: evolution of antifreeze gene in arctic fish

5% of the human genome is foundto be recently-duplicated largesegments (>500bp, identity>95%).[JA Bailey, Science, 2002]

The duplicated regions createmosaic structure.

Some of the duplicated segmentscontain new genes.

Human genome: gene duplications

Insertion sequences

Only encode for transposase, no exogenous genes.

Transposons

Carry both transposase and exogenous genes (e.g. drug resistant genes).

Non-autonomous transposable elements

Do not carry transposase itself, depend on other autonomous transposable elements.

Retroelements

Carry reverse transcriptase.

-Retrovirus

-Retroposons

-Retrotrnasposons

Mobile Elements (selfish DNA)

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Example: transposons

Transposons disrupt genes but can also carry genes around chromosome and amongdifferent cells.

Chromosome rearrangements

Example: comparison of bacterial genomes

BACTERIA ARCHAEA

Aquifex

Thermus

Thermotoga

Gram-posit

ive bac

teria

Green su

lfur b

acter

ia

Purple bac

teria

Cyanobac

teria

Flavobac

teria

pJP78pSL17

Pyrodict

ium

Sulfolobus

Thermoproteu

s

Methan

opyrus

Methan

obacter

ium

Thermoco

ccus

Archae

oglobus

Haloco

ccus

Methan

ococc

us

When genes are transferred laterally,they move between species that are

not necessarily closely related

Figure 16.6

Lateral gene transfer - very important mechanisms in prokaryotes!

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1 Transformation: uptake of DNA from environment2 Transduction: DNA transfer by viruses3 Conjugation: plasmid transfer between bacterial cells

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3

Mechanisms of lateral gene transfer Recognizing laterally transferred DNA:- different GC content- “new” DNA in related organisms- phylogenetic differences

Example:Pathogenicity islands - many pathogens acquire genes from other bacteria

16 S rRNA gene Protein coding generevealing function of

organism in environment

BAC clone obtained directly from environment

Environmental Genomics - applying genomic sequencing to DNA directlyobtained from the environment ProteorhodopsinProteorhodopsin::

A new way to convertA new way to convertsolar energy tosolar energy tochemical energy inchemical energy inthe oceanthe ocean

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