Comparative Genomics: The study of genome conservation

and variation among organisms

Chromosome numberChromosome morphology

Gene numberGenome sizeGene order

Measures of Genome Size

C value : amount of DNA in the haploid genome, generally measured in picograms or in base pairs (Kb or Mb)

Range of C Values in Prokaryotes

Taxon Genome Size (Kb) Ratio

Bacteria 580 - 13,200 23 Mollicutes 580 - 2,200 4 Gram negatives 650 - 9,500 15 Gram positives 1,600 - 11,600 7 Cyanobacteria 3,100 - 13,200 4Archaea 1,600 - 4,100 3

~ 20 fold range in genome size

Genome Size (x 106 bp)

1000

2000

3000

4000

5000

GeneNumber

Gene Number and Genome Size in 12 CompletelySequenced Bacterial Species

C value : So, what about eukaryotes?

• In general, more DNA• Much greater variation in genome size

• 80,000 fold range across eukaryotes• Largest range observed among unicellular protists (20,000 fold)• 3,000 fold range in animals• No relationship between c value and organismal complexity:

the c value paradox

Species C value (Kb)Saccharomyces cerevisiae 12,000Caenorhabditi elegans 80,000Drosophila melanogaster 180,000Strongylocentrotus purpuratus 870,000Gallus domesticus 1,200,000Canis familiaris 2,900,000Rattus norvegicus 2,900,000Xenopus laevis 3,100,000Homo sapiens 3,600,000Nicotiana tabacum 3,800,000Ambystoma tigrinum 32,000,000Pinus resinosa 68,000,000Lepidosiren paradoxa 120,000,000Ophioglossum petiolatum 160,000,000Amoeba dubia 690,000,000

C values from eukaryotic organisms ranked by genome size

What explainsthe C value paradox?

Polyploidization: complete genome duplication

Role of Regional Duplications in Genome Evolution

Genome size and amount of heterochromatin

98% of variance explained

Genic Fraction vs Genome Size

Synteny : Occurence of two or more genes on a chromosome.

Conserved Synteny : Synteny of orthologous genes between species.

Terms for Comparing Gene Order

A B C D E F

I H G J K L M

D E F G H I J K L M

translocation

A B C

A B C D E F G

G H I J K L M

inversion

Speciation

Ancestral Condition

1 2 3 4 5 6 a b 7 8 9

6 5 4 c d e 9 8 7 1 2 3

1 2 3 4 5 6 7 8 9

6 5 4 9 8 7 1 2 3

Delete

(a,b) & (c,d,e)

Reconstructing the Evolution of Gene Order

1 2 3 4 5 6 7 8 9

6 5 4 9 8 7 1 2 3

1 4 72 5 83 6 9

6 9 15 8 24 7 3

Bundle1, 2 & 34, 5 & 67, 8 & 9

Invert

(1 2 3) & (4 5 6)

6 3 75 2 84 1 9

6 9 15 8 24 7 3

1 2 3 4 5

3 5 2 4 1

1 2 3 4 5

3 2 5 4 1

Invert

2 & 5

Invert

(541)

1 2 3 4 5

3 2 1 4 5

Invert

(321)

1 2 3 4 5

3 2 1 4 5

E = D + R

Evolutionary EditDistance

= Minimal #Deletions +

Minimal #Rearrangements

OTUsb Hs Gg Sp Ap Po Dy As

Hs(human) 1 18 16 19 13 25

Gg(chick) 0 19 17 17 12 26

Sp(urchin) 0 0 2 1 26 27

Ap(starfish) 4 4 4 1 22 24

Po(starfish) 1 1 1 5 23 24

Dy(fruitfly) 0 0 0 4 1 28

As(roundworm) 1 1 1 5 1 1

Deletion Distance

Rearrangement Distance

Data from mitochondrial genomes

300

65

100

(0.1)(1.1)(0.2)

Chicken Mouse Human

Rate of Chromosome Rearrangement(per million years)

Ehrlich et al (1997) : Gene rearrangements occur with amazing rapidity among mammals; rate of synteny disruption 25 times higher in mouse lineage; interchromosomal rearrangements are common.

Chicken 128 72

Mouse 152 171

Human 96 195

Chicken Mouse Human

Total number of autosomalconserved syntenies

Total number of rearrangements

Chromosomal Distribution of Orthologous Genes

Human MouseCount 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Count 1 2 3 4 5 6 7 8 9 10 11 12 13 14chr1 1 1 6 11 0 6 3 0 3 12 5 1 2 0 chr1 2 1 2 1 2 0 0 1 1 5 3 1 1 0chr2 0 1 6 0 5 1 0 2 1 0 0 0 2 0 chr2 5 0 7 1 2 1 3 1 2 0 0 1 1 0chr3 0 0 15 1 1 0 2 5 1 0 1 1 0 0 chr3 3 1 3 7 0 0 0 2 3 6 2 0 0 0chr4 0 3 1 0 0 0 0 0 0 0 0 0 0 0 chr4 0 4 0 1 1 6 3 1 0 2 1 0 0 0chr5 7 5 0 0 0 1 0 0 0 0 0 0 0 0 chr5 2 1 5 0 2 0 0 3 0 0 0 0 0 0chr6 0 3 2 1 0 2 0 0 3 0 1 1 2 0 chr6 4 2 11 1 1 0 0 2 11 0 1 0 0 1chr7 1 0 9 0 3 0 0 2 7 0 2 0 0 1 chr7 5 0 9 8 0 0 0 0 0 0 1 0 0 0chr8 1 3 1 0 0 1 0 2 0 0 0 0 0 0 chr8 3 3 2 4 0 0 0 1 0 2 0 0 0 0chr9 0 7 0 2 0 1 3 0 0 0 0 0 0 0 chr9 5 1 3 0 0 6 2 1 1 1 1 0 1 0chr10 1 0 6 0 0 0 4 3 0 0 0 0 0 0 chr10 3 1 1 4 3 0 3 1 5 0 0 0 1 0chr11 1 0 11 2 0 0 0 1 2 0 1 0 1 0 chr11 12 1 11 3 3 0 0 6 2 0 13 0 2 0chr12 11 1 2 1 1 0 0 4 11 0 1 0 0 0 chr12 2 1 5 1 0 0 0 0 1 0 1 0 0 7chr13 0 0 0 0 0 0 0 0 1 0 0 1 0 0 chr13 0 3 4 3 0 0 0 0 2 0 0 0 1 0chr14 0 0 6 2 0 0 0 0 0 0 1 0 0 6 chr14 2 0 6 1 0 0 2 2 0 0 1 1 0 0chr15 1 1 2 1 0 8 0 0 1 1 0 0 0 0 chr15 7 4 4 0 0 2 0 0 3 0 1 0 0 0chr16 4 0 6 3 0 0 0 0 0 2 1 0 0 0 chr16 1 0 0 0 1 0 0 2 1 0 0 1 0 0chr17 7 1 7 3 2 0 0 2 0 0 12 0 0 0 chr17 2 1 5 2 0 1 0 0 1 0 1 1 1 0chr18 0 5 0 0 0 0 0 0 0 0 1 0 0 0 chr18 0 2 0 0 0 0 0 0 0 0 1 1 0 0chr19 8 0 3 15 1 0 0 1 0 0 0 0 0 0 chr19 0 3 12 2 0 1 0 0 0 0 0 0 0 0chr20 7 1 2 1 0 0 0 1 0 0 0 1 1 0 chrX 0 2 3 0 0 0 0 1 0 0 0 3 1 0chr21 0 0 0 1 3 0 0 0 0 0 0 0 0 0chr22 1 0 2 0 0 0 0 0 4 0 0 0 0 0chrX 0 2 3 0 0 0 0 1 0 0 0 3 1 0chrY 0 0 0 0 0 0 0 0 0 0 0 1 0 0

Chicken RatCount 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Count 1 2 3 4 5 6 7 8 9 10 11 12 13 14chr1 5 2 9 1 0 2 0 2 7 0 2 3 1 0 chr1 5 4 18 8 0 0 0 1 0 0 0 0 2 0chr2 1 8 8 2 0 0 1 1 0 0 3 0 0 0 chr2 2 5 0 4 0 1 0 1 1 5 0 0 0 0chr3 4 0 4 1 0 2 0 0 1 0 0 0 5 0 chr3 3 1 3 0 1 1 2 2 0 0 2 0 1 0chr4 0 4 1 0 0 1 2 0 0 0 0 0 0 0 chr4 4 0 8 1 1 0 1 1 5 0 3 0 0 0chr5 1 0 4 4 0 0 0 1 1 0 0 0 0 6 chr5 2 2 1 0 2 3 1 1 0 1 0 0 0 0chr6 0 0 1 0 0 0 3 1 0 0 1 0 0 0 chr6 2 1 4 0 1 0 0 1 0 0 1 0 1 2chr7 0 0 1 0 7 0 0 0 2 0 0 1 0 0 chr7 3 0 4 4 0 0 0 2 6 0 2 0 0 0chr8 1 1 0 0 0 0 0 0 0 11 0 0 0 0 chr8 4 0 2 3 0 5 1 1 2 1 0 0 0 0chr9 0 0 0 2 4 0 0 3 0 0 0 0 0 0 chr9 0 1 0 0 2 0 0 0 0 0 0 0 0 0chr10 1 0 0 3 0 6 0 0 1 1 0 0 0 0 chr10 10 2 8 2 0 0 0 2 1 0 7 0 0 0chr11 0 1 0 3 0 0 1 0 0 1 0 0 0 0 chr11 2 0 0 1 1 1 0 1 0 0 1 1 0 0chr12 0 0 7 0 0 0 0 0 2 0 1 0 0 0 chr12 0 1 5 0 2 1 0 1 0 1 2 0 0 0chr13 5 0 0 0 0 0 0 1 0 0 0 0 0 0 chr13 1 1 0 0 0 0 0 0 0 3 0 0 0 0chr14 1 0 9 0 0 0 0 0 1 0 0 0 0 1 chr14 0 1 0 0 0 0 0 1 1 0 0 0 0 0chr15 0 0 0 0 0 1 0 1 2 0 0 0 0 0 chr15 2 0 5 1 0 0 1 0 0 0 0 0 0 0chr16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 chr16 2 0 3 1 0 0 1 2 1 0 0 0 0 0chr17 1 0 0 0 0 0 4 0 0 0 0 0 0 0 chr17 2 0 1 1 0 0 0 0 2 0 0 0 0 0chr18 6 1 4 0 0 0 0 0 0 0 0 0 0 0 chr18 2 3 1 1 1 0 0 0 0 0 1 1 0 0chr19 2 0 0 0 4 0 0 3 0 0 0 0 0 0 chr19 0 1 2 1 0 0 0 1 0 1 0 0 0 0chr20 5 1 0 1 0 0 0 0 0 0 1 0 0 0 chr20 0 0 0 0 0 0 0 0 1 0 1 0 1 0chr21 2 0 0 0 0 0 2 0 0 0 0 0 0 0 chrX 0 1 3 0 0 0 0 1 0 0 0 0 1 0chr22 0 0 0 0 0 0 0 1 0 0 0 0 0 0chr23 0 0 0 0 0 4 0 0 0 0 0 0 0 0chr24 1 0 0 1 0 0 0 0 2 0 0 0 0 0chr26 0 0 1 0 0 0 0 0 1 0 2 0 0 0chr27 0 1 0 0 0 0 0 0 0 0 5 0 0 0chr28 1 0 3 3 0 0 0 0 0 0 0 0 0 0chrZ 1 7 0 1 0 1 0 0 0 0 0 0 0 0

HUMAN

CHICKEN

MOUSE

RAT

Salamander Salamander

N = 402Refseq database size = 21,098

N = 338Refseq database size = 16,800

N = 338Refseq database size = 11,348

N = 236Refseq database size = 12,427

Number of Conserved Syntenies

Comparison #a #b

Human 69 28Mouse 82 24Chicken 52 17Rat 58 14

#a based on 2 or more orthologues

#b based on 4 or more orthologues

Spatial Distribution of Orthologous Loci :

Segmental Homology

Lg1 Lg2 Lg3 Lg14

Salamander Genome

HUMAN

GENOME(1-23)

white met melanoid

Lg1 Lg2 Lg3 Lg14

Salamander Genome

CHICKEN

GENOME(1-23)

Conserved Synteny based upon 3 or more genes

white met melanoid

Candidate Genes

met

white

sex

melanoid

Cross-Referencing

Chromosomal Sex Determination

Birds Mammals

300-350 mya

ZZ - ZWMale Female

XY - XXMale Female

Sry Locus:testes determining

factor

?

Ohno’s Hypothesis

Bird and Mammalian Sex Chromosomes were derivedfrom the same ancestral autosomal pair

ZW Birds

X

Y

Mammals

A

A XX

ZZ

Ohno’s Hypothesis Predicts:

The same orthologous loci will be identifiedbetween the sex chromosomes of

birds and mammals (i.e. conserved synteny)

CHD-WATPA1-W

p

q20 cM

ATPA1-Z

GHR

OTC

CHD-ZCHRNB3

ALDOB

GGTB2 IREB1

Chick W Chick Z Human Mouse

18q

5p

Xp

5q8p

9q

9p9

18

15

17

4

44

Fridolfsson et al 1998

Chick Z Human 9

p

q

IFN1/IFNA1IFN2.IFNB1

DMRT1

VLDLRBRM/SMARCA2

NTRK2GGTB2/B4GALT1

ACO1TMOD

ALDOBPTCH

AMBPABL1AK1

RPL7ACD39L1

Comparative Locations of Orthologous Loci

p

q

Chick microchromosome(linkage group E41W17)

Nanda et al (1999)

Conclusion

Bird and Mammalian Sex Chromosomes Evolved Independently from Different

Autosomal Precursors