Genome Evolution Xuhua Xia - PowerPoint Presentation

Slide1

Genome Evolution

Xuhua Xiaxxia@uottawa.cahttp://dambe.bio.uottawa.ca

Slide2

Definitions

Genome: the entire complement of genetic material carried by an individualTranscriptome with two definitions:the entire set of transcribable sequences from the genome (operationally all RNA sequences from annotated productive genes in a genome)

all transcripts and their abundances in a particular cell or tissueProteome with two definitions:

the entire set of proteins encoded by the genome (operationally theset of proteins translated from annotated CDSs in a genome)all proteins and their abundances in a particular cell of tissue.

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Genomic Evolution

Genomic differences:Genome size variationGenomic GC variationVariation in strand asymmetryGenomic gene content variation

Genomic changes and pathogenecityContributing factors

MutationSelection

Slide4

Fig. 8.7

Scenario showing possible events following whole genome duplication

26 genes on 2 chromosomes

... so that 52 genes on 4 chromosomes

hybrid

E’ and e’ genes generated by cross-over within gene E

autopolyploid

(if from same set of chromosomes)

Outcome: 36 genes on 4 chromosomes

A B D E F H...

b c e g h...

b c

E’

F H...

A B D

e’

g h

Crossing over

Translocation

Loss of copies of certain genes

Tetraploidization

Comparative genomics: Prof

. David Sankoff in Department of Mathematics, University of Ottawa

Slide5

Kellis

Nature

428:617, 2004

Evidence for whole genome duplication in ancestor of yeast

see also Fig.8.6

Recombination between paralogous copies (eg. 3)

~ 100 million years ago?

Genome duplication

Massive gene loss (& pseudogenes with x), but some genes retained

Sister DNA segments retain different genes (except for 3 and 13)

Typically translocation of some genes during evolution (as well as some residual linkages)

Deduced from sequence comparisons, including with yeast relative:

Kluyveromyces

(middle pink schematic)

No genome duplication in

Kluyveromyces

lineage

Slide6

Arabidopsis ~ 135 ~ 15%

rice ~420 ~ 35%

wheat ~ 1700 ~ 80%

rye ~ 7900 ~ 90%

% repetitive elements

Within grasses,

> 30-fold range in genome size

Kellogg & Bennetzen

Am J Bo

t 91:1709, 2004

In plants: “The ups and downs of genome size evolution” due to transposable elements, DNA segment duplications…

Haploid genome size (

Mbp

)

“Evolution canyon”, Israel

Environmental stress

conditions (hot & dry) trigger

retrotransposon

copy number increase in barley

South side (hot & dry)

~

22,000

copies BARE-1 (TE) in barley

North side ~

8000 BARE-1 copies

Kalendar PNAS 97: 6603 (2000)

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Rickettsia prowazekii

Andersson

Nature

396: 133, 1998

a-

proteobacteria – respiratory chain very similar to mitochondrial one

causative agent of typhus

intracellular parasite

Genome reduction in obligate parasites

One lineage in Rickettsiales has degenerated so much: mitochondria

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Ups and downs of mitochondrial genome

Reclinomonas americana

: a heterotrophic flagellate, with a large mitochondrial genome:

69034 bp97 genes4 genes specifying a multisubunit, eubacterial-type RNA polymerase

Vertebrate mitochondria:

~16500 bp

13 protein-coding genes

2 rRNA genes

~22 tRNA genes

Mitosome in Giardia and Microsporidia species that do not have mitochondria:

Mostly

likely derived from mitochondria, but contains no DNA (contrary to an early report

) so missing the most conclusive evidence

Ancestors of Giardia and Microsporidia species have mitochondria

It shares with mitochondria a number of nucleus-encoded proteins imported from cytosol, and these proteins use targeting sequences similar to those used by nucleus-encoded mitochondrial proteinsMitochondrial targeting sequences are recognized sequentially by a series of protein translocases such as TOM and TIM complexes. Some mitosomes contain proteins homologous to TOM and TIM proteins.

Nature 426:172,2003

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Genomic Evolution

Genomic differences:Genome size variationGenomic GC variationVariation in strand asymmetryGenomic gene content variation

Genomic changes and pathogenecity

Contributing factorsMutationSelection

Slide10

Fig. 8.26

Wide variation in GC content among bacterial genomes

consequences of genomic GC content for bacterial codon usage patterns?

third position of codon

2d position of codon

- because functional constraint on 2d (& 1

st

) codon positions...

...not as strong correlation with overall genomic % G+C content

Fig.8.29: selection and mutation hypotheses

Solid lines represent 1

st

, 2d & 3

rd

positions of codons

Genome GC content (%)

Codon GC content (%)

first position

divergence time

genome size

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How would genomic GC change with increasing temperature?

Experimental evolution

Culturing

Pasterrella multocida under increasing temperature for ~14,400 generations. Will the resulting strain have higher GC?RAPD with AT-rich and GC-rich primers:AATTCCGGATCCGGCCGGCG......Xia et al. 2002. Genetics 161: 1385–1394

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How would genomic GC change with increasing temperature?

N_A+T

N_C+G

Ni_A

Ni_

G

AATTCCGGAT

6

4

3

2

CCGGCCGGCG

0

10

4

8……

Rationale:Xia et al. 2002. Genetics 161: 1385–1394 Strain A: original virulent strainStrain G: derived vaccine strain after culturing in increasing temperature for 14,400 generations

StrainAStrainG

S_A+T1812S_C+G

5288Results from one pair of primers

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No significant difference between the original and the temperature-adapted strain

Xia et al. 2002.

Genetics 161: 1385–1394

R1

R2

StrainA

26.455%

73.545%

25.215%

74.785%

StrainG

29.462%

70.538%

29.130%

70.870%

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However, temperature has a significant effect on GC content of ribosomal RNA genes in bacterial and Archaeal species

Wang, H. C., Xia, X. , D. Hickey. 2006. Journal of Molecular Evolution 63(1):120-126

E.coli 16S rRNA

C - G

A - U

U - A

A

-

U

C - G

G - C

U - A

G - C

Stem_CG

%

Stem_Length

mesophilic

Low

Short

moderately thermophilic

Medium

Medium

hyperthermophilic

HighLong

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Genomic Evolution

Genomic differences:Genome size variationGenomic GC variationVariation in strand asymmetry

Genomic gene content variationGenomic changes and pathogenecity

Contributing factorsMutationSelection

Slide16

Single-origin replication in bacteria

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Strand-switching and evolutionary rate in vertebrate mtDNA

Fig. 3-11.

Trees constructed from four tRNA genes (a, b, c, and d), with the topology constrained by the COX1 gene. Each tree has one lineage (

bolded) where the tRNA gene has switched strand, which is associated with a dramatically increased evolutionary rate. (e) and (f) illustrate the identification of strand-switching events, with arrows pointing in the 5’ to ‘3 direction.

Xia

X

2012 In

: Singh RS, Xu J, Kulathinal RJ, editors.

Evolution in the fast lane: Rapidly evolving genes and genetic systems

.

Oxford

University Press. pp. 73-82

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Genomic Evolution

Genomic differences:Genome size variationGenomic GC variationVariation in strand asymmetry

Genomic gene content variationGenomic changes and pathogenecity

Contributing factorsMutationSelection

Slide19

E.coli

~

1125

pseudogenes

in

M. leprae

!!

but duplicated genes would expand the genome size...

Bacterial and archaebacterial genomes

Possible explanations for species that are outliers?

~1000 genes/Mb = 1 gene/Kb

Parasites

Wrong number, currently at 1700

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Fig. 8.15

Multicellular eukaryotes

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Fig. 8.1

E. coli

Haemophilus

influenzae

Mycoplasma

genitalium

Search for “minimal” bacterial genome

eg. archaeal-specific

(no detectable homologues in other lineages)

=

350

Woese

PNAS

97:3302, 2000

eg. eukaryotic-specific

=

915

(or

315

if include Giardia - parasite with reduced gene set)

Hartman

PNAS

99:1420, 2002

Search for “signature proteins” distinctive for 3 “domains of life”Search for a “minimal” genome

Pitfalls: the same function can be performed by totally different genes.

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Genomic Evolution

Genomic differences:Genome size variationGenomic GC variationVariation in strand asymmetry

Genomic gene content variationGenomic changes and pathogenecity

Contributing factorsMutationSelection

Slide23

Parkhill

Nature

413:523, 2001

Yersinia pestis

Genome fluidity

- inversion/translocation of chromosomal segments

- intragenomic recombination at IS element sites

Gene acquisition and decay

- lateral transfer of genes from other bacteria & viruses

eg. surface antigens, virulence factors involved in pathogenicity against

both mammals and insects

Y. pestis has 149 pseudogenes

Obligate parasites often undergo “reductive evolution” during colonization of niche

Strand bias of G vs. C

(purple vs. green)

“The genome of the bacterium that causes the plague is

highly dynamic

and scarred by

genes acquired

from other organisms.”

“pathogenicity islands”

“Use it or lose it…”

Aside: free-living bacteria (or archaea) rarely have pseudogenes

Can help identify where DNA rearrangements have occurred

Slide24

Avian influenza virus – RNA genome (8 segments)

- used dataset of 414 hemagglutin (HA) nucleotide sequences in phylogeographic analysis

Lebarbenchon & Stallknecht

Virology J

8:328, 2011

- rapid evolution both through nt mutation & reassortment of genome segments

“Segment 4” of genome encodes hemagglutinin (HA) – major surface glycoprotein

Genome recombination

Phylogenetic incongruence test