Download Slides - Salamander Genome Project

Comparative Genomics:
The study of genome conservation
and variation among organisms
Chromosome number
Chromosome morphology
Gene number
Genome size
Gene 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)
Bacteria
Mollicutes
Gram negatives
Gram positives
Cyanobacteria
Archaea
580 - 13,200
580 - 2,200
650 - 9,500
1,600 - 11,600
3,100 - 13,200
1,600 - 4,100
Ratio
23
4
15
7
4
3
~ 20 fold range in genome size
Gene Number and Genome Size in 12 Completely
Sequenced Bacterial Species
5000
4000
Gene 3000
Number
2000
1000
Genome Size (x 106 bp)
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
C values from eukaryotic organisms ranked by genome size
Species
Saccharomyces cerevisiae
Caenorhabditi elegans
Drosophila melanogaster
Strongylocentrotus purpuratus
Gallus domesticus
Canis familiaris
Rattus norvegicus
Xenopus laevis
Homo sapiens
Nicotiana tabacum
Ambystoma tigrinum
Pinus resinosa
Lepidosiren paradoxa
Ophioglossum petiolatum
Amoeba dubia
C value (Kb)
12,000
80,000
180,000
870,000
1,200,000
2,900,000
2,900,000
3,100,000
3,600,000
3,800,000
32,000,000
68,000,000
120,000,000
160,000,000
690,000,000
What explains
the 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
Terms for Comparing Gene Order
Synteny : Occurence of two or more genes on a
chromosome.
Conserved Synteny : Synteny of orthologous genes
between species.
A
B
C
D
G
H
I
J
E
K
F
L
M
Ancestral Condition
Speciation
A B C D E F G
D E F GHIJKLM
IHG J K L M
A B C
inversion
translocation
Reconstructing the Evolution of Gene Order
1 2 3 4 5 6 a b 7 8 9
1 2 3 4 5 6 7 8 9
Delete
(a,b) & (c,d,e)
6 5 4 c d e 9 8 7 1 2 3
6 5 4 9 8 7 1 2 3
1 2 3 4 5 6 7 8 9
Bundle
Invert
1, 2 & 3
4, 5 & 6
7, 8 & 9
6 5 4 9 8 7 1 2 3
6 3 7
5 2 8
4 1 9
1 4 7
2 5 8
3 6 9
(1 2 3) & (4 5 6)
6 9 1
5 8 2
4 7 3
6 9 1
5 8 2
4 7 3
12345
12345
Invert
Invert
32541
Evolutionary Edit =
Distance
(321)
32145
E=
12345
Invert
(541)
2&5
35241
12345
32145
D + R
Minimal # +
Deletions
Minimal #
Rearrangements
Data from mitochondrial genomes
Rearrangement Distance
OTUsb
Hs
Hs(human)
Gg
Sp
Ap
Po
Dy
As
1
18
16
19
13
25
19
17
17
12
26
2
1
26
27
1
22
24
23
24
Gg(chick)
0
Sp(urchin)
0
0
Ap(starfish)
4
4
4
Po(starfish)
1
1
1
5
Dy(fruitfly)
0
0
0
4
1
As(roundworm)
1
1
1
5
1
Deletion Distance
28
1
Rate of Chromosome Rearrangement
(per million years)
300
100
65
(0.2)
Chicken
(1.1)
Mouse
(0.1)
Human
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.
Total number of
rearrangements
Chicken
Chicken
Mouse
128
Mouse
152
Human
96
Total number of autosomal
conserved syntenies
Human
72
171
195
Chromosomal Distribution of Orthologous Genes
HUMAN
N = 402
Refseq database
size = 21,098
Count
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
1
1
0
0
0
7
0
1
1
0
1
1
11
0
0
1
4
7
0
8
7
0
1
0
0
Count
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chr23
chr24
chr26
chr27
chr28
chrZ
1
5
1
4
0
1
0
0
1
0
1
0
0
5
1
0
1
1
6
2
5
2
0
0
1
0
0
1
1
Human
Salamander
2
3
4
1
6 11
1
6
0
0 15
1
3
1
0
5
0
0
3
2
1
0
9
0
3
1
0
7
0
2
0
6
0
0 11
2
1
2
1
0
0
0
0
6
2
1
2
1
0
6
3
1
7
3
5
0
0
0
3 15
1
2
1
0
0
1
0
2
0
2
3
0
0
0
0
5
0
5
1
0
0
0
3
0
0
0
0
1
0
0
0
0
2
0
1
0
3
0
0
0
2
2
8
0
4
0
0
0
1
0
0
1
0
0
0
0
0
0
1
0
1
0
0
0
0
0
1
0
7
5
0
0
0
0
0
0
7
0
4
0
0
0
0
0
0
0
0
0
4
0
0
0
0
0
0
0
0
0
6
6
1
0
0
1
2
0
1
1
0
0
0
0
0
8
0
0
0
0
0
0
0
0
0
7
3
0
2
0
0
0
0
0
3
4
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mouse
Salamander
8
9 10 11 12 13 14
0
3 12
5
1
2
0
2
1
0
0
0
2
0
5
1
0
1
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
3
0
1
1
2
0
2
7
0
2
0
0
1
2
0
0
0
0
0
0
0
0
0
0
0
0
0
3
0
0
0
0
0
0
1
2
0
1
0
1
0
4 11
0
1
0
0
0
0
1
0
0
1
0
0
0
0
0
1
0
0
6
0
1
1
0
0
0
0
0
0
2
1
0
0
0
2
0
0 12
0
0
0
0
0
0
1
0
0
0
1
0
0
0
0
0
0
1
0
0
0
1
1
0
0
0
0
0
0
0
0
0
4
0
0
0
0
0
1
0
0
0
3
1
0
0
0
0
0
1
0
0
Count
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chrX
1
2
5
3
0
2
4
5
3
5
3
12
2
0
2
7
1
2
0
0
0
2
3
1
2
0
7
1
3
4
0
1
5
2 11
0
9
3
2
1
3
1
1
1 11
1
5
3
4
0
6
4
4
0
0
1
5
2
0
3 12
2
3
4
1
1
7
1
0
1
8
4
0
4
3
1
3
1
0
0
2
0
2
0
5
2
2
0
1
2
1
0
0
0
3
3
0
0
0
0
1
0
0
0
0
Count
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chrX
1
5
2
3
4
2
2
3
4
0
10
2
0
1
0
2
2
2
2
0
0
0
2
3
4 18
5
0
1
3
0
8
2
1
1
4
0
4
0
2
1
0
2
8
0
0
1
5
1
0
1
0
0
5
0
3
0
1
3
1
1
2
0
0
1
3
4
8
4
0
1
0
0
4
3
0
2
1
0
0
0
1
1
1
1
1
0
0
5
0
0
1
1
2
1
0
0
2
0
1
2
0
0
0
0
0
1
0
0
0
Chicken
CHICKEN
N = 338
Refseq database
size = 11,348
3
9
8
4
1
4
1
1
0
0
0
0
7
0
9
0
0
0
4
0
0
0
0
0
0
1
0
3
0
4
1
2
1
0
4
0
0
0
2
3
3
0
0
0
0
0
0
0
0
1
0
0
0
1
0
0
3
1
6
2
0
2
1
0
0
0
0
0
6
0
0
0
0
1
0
0
0
0
0
0
0
4
0
0
0
0
1
7
0
1
0
2
0
3
0
0
0
0
1
0
0
0
0
0
4
0
0
0
2
0
0
0
0
0
0
0
8
2
1
0
0
1
1
0
0
3
0
0
0
1
0
1
0
0
0
3
0
0
1
0
0
0
0
0
0
6
0
1
0
6
0
0
0
0
6
0
0
0
0
0
2
0
1
0
1
0
7
0
3
0
3
0
0
0
0
2
3
0
0
0
2
0
0
0
0
0
0
8
9 10 11 12 13 14
1
1
5
3
1
1
0
1
2
0
0
1
1
0
2
3
6
2
0
0
0
1
0
2
1
0
0
0
3
0
0
0
0
0
0
2 11
0
1
0
0
1
0
0
0
1
0
0
0
1
0
2
0
0
0
0
1
1
1
1
0
1
0
1
5
0
0
0
1
0
6
2
0 13
0
2
0
0
1
0
1
0
0
7
0
2
0
0
0
1
0
2
0
0
1
1
0
0
0
3
0
1
0
0
0
2
1
0
0
1
0
0
0
1
0
1
1
1
0
0
0
0
1
1
0
0
0
0
0
0
0
0
0
1
0
0
0
3
1
0
7
0
0
2
1
1
0
0
1
0
0
0
0
0
0
1
1
0
0
0
0
0
8
1
1
2
1
1
1
2
1
0
2
1
1
0
1
0
2
0
0
1
0
1
MOUSE
N = 338
Refseq database
size = 16,800
Rat
9 10 11 12 13 14
7
0
2
3
1
0
0
0
3
0
0
0
1
0
0
0
5
0
0
0
0
0
0
0
1
0
0
0
0
6
0
0
1
0
0
0
2
0
0
1
0
0
0 11
0
0
0
0
0
0
0
0
0
0
1
1
0
0
0
0
0
1
0
0
0
0
2
0
1
0
0
0
0
0
0
0
0
0
1
0
0
0
0
1
2
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
2
0
0
0
0
0
1
0
2
0
0
0
0
0
5
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
6
0
1
1
0
3
0
0
5
0
0
1
1
0
0
0
0
0
0
0
0
0
9 10 11 12 13 14
0
0
0
0
2
0
1
5
0
0
0
0
0
0
2
0
1
0
5
0
3
0
0
0
0
1
0
0
0
0
0
0
1
0
1
2
6
0
2
0
0
0
2
1
0
0
0
0
0
0
0
0
0
0
1
0
7
0
0
0
0
0
1
1
0
0
0
1
2
0
0
0
0
3
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
2
0
0
0
0
0
0
0
1
1
0
0
0
1
0
0
0
0
1
0
1
0
1
0
0
0
0
0
1
0
RAT
N = 236
Refseq database
size = 12,427
Number of Conserved Syntenies
Comparison
#a
#b
Human
Mouse
Chicken
Rat
69
82
52
58
28
24
17
14
#a based on 2 or more orthologues
#b based on 4 or more orthologues
Spatial Distribution of Orthologous Loci :
Segmental Homology
H
U
M
A
N
G
E
N
O
M
E
(1-23)
Lg1
white
Lg2
Lg3
met
Lg14
Salamander Genome
melanoid
Conserved Synteny based upon 3 or more genes
C
H
I
C
K
E
N
G
E
N
O
M
E
(1-23)
Lg1
white
Lg2
Lg3
met
Lg14
Salamander Genome
melanoid
Candidate Genes
Cross-Referencing
sex
melanoid
white
met
Chromosomal Sex Determination
ZZ - ZW
Male
Female
Birds
Mammals
XY - XX
Male
?
Female
Sry Locus:
testes determining
factor
300-350 mya
Ohno’s Hypothesis
Bird and Mammalian Sex Chromosomes were derived
from the same ancestral autosomal pair
Z
W
Birds
Z
Z
A
A
X
X
X
Y
Mammals
Ohno’s Hypothesis Predicts:
The same orthologous loci will be identified
between the sex chromosomes of
birds and mammals (i.e. conserved synteny)
Chick W
Chick Z
p
CHD-W
ATPA1-W
q
Human
Mouse
ATPA1-Z
18q
18
GHR
5p
15
OTC
Xp
CHD-Z
CHRNB3
5q
ALDOB
9q
4
GGTB2
IREB1
9
9p
4
4
17
8p
20 cM
Fridolfsson et al 1998
Comparative Locations of Orthologous Loci
Chick Z
Human 9
IFN1/IFNA1
IFN2.IFNB1
p
DMRT1
q
VLDLR
BRM/SMARCA2
NTRK2
GGTB2/B4GALT1
ACO1
TMOD
ALDOB
PTCH
Chick microchromosome
(linkage group E41W17)
p
q
AMBP
ABL1
AK1
RPL7A
CD39L1
Nanda et al (1999)
Conclusion
Bird and Mammalian Sex Chromosomes
Evolved Independently from Different
Autosomal Precursors