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Ambystoma Linkage Map - PowerPoint PPT Presentation


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Chromosome-level Mutation. A B C D E F. G H I J K L M. A B C D E F G. D E F G H I J K L M. I H G J K L M. A B C. inversion. translocation.

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slide1

Chromosome-level Mutation

A B C D E F

G H I J K L M

A B C D E F G

D E F G H I J K L M

I H G J K L M

A B C

inversion

translocation

slide2

Processes of Gene Rearrangement

A B C D C D E

duplication

B A C D E

A B C D

terminal deletion

pericentric inversion

A B C D E

Eliminate

A D C B E

paracentric inversion

A B C E

A B C D E

interstitial deletion

breakage

slide3

Exchange of Genetic Information

A B C D E F

W X Y Z

Translocation

Centric fusion

Z Y X C D E F

A B C X Y Z

W D E F

slide4

Terms for Comparing Gene Order

Synteny : Occurence of two or more genes on a

chromosome.

Conserved Synteny : Synteny of orthologous genes

between species.

ambystoma linkage map
Ambystoma Linkage Map

5251 cM (~93%)

slide6

Salamander Genome….BIG!

Human

Salamander

Reptile

slide7

Genome-wide recombination is not proportional

to chromosome # in Ambystoma

genome Chom. Chrom. obligatory proportion

size (Gbp) # Arms Map (cM) cM / Mb(A# * 50cM) obligatory cM/arm

Mouse 2.7 20 20 1361 0.5 1000 0.73 68.1

Rat 2.6 21 33 1749 0.7 1050 0.94 53.0

Human 3.0 23 46 3615 1.2 1150 0.64 78.6

Chicken 1.2 38 44 3800 3.2 1900 0.58 86.4

Ambystoma 30.0 14 28 5152 0.2 700 0.27 184.0

chromosomal distribution of orthologous genes
Chromosomal Distribution of Orthologous Genes

Salamander

Salamander

MOUSE

HUMAN

N = 338

Refseq database

size = 16,800

N = 402

Refseq database

size = 21,098

CHICKEN

RAT

N = 338

Refseq database

size = 11,348

N = 236

Refseq database

size = 12,427

slide9

Number of Conserved Syntenies

Comparison #a #b

Human 69 28

Mouse 82 24

Chicken 52 17

Rat 58 14

#a based on 2 or more orthologues

#b based on 4 or more orthologues

spatial distribution of orthologous loci segmental homology
Spatial Distribution of Orthologous Loci : Segmental Homology

H

U

M

A

N

G

E

N

O

M

E

(1-23)

Lg1

Lg2

Lg3

Lg14

white

met

melanoid

Salamander Genome

slide11

Conserved Synteny based upon 3 or more genes

C

H

I

C

K

E

N

G

E

N

O

M

E

(1-23)

Lg1

Lg2

Lg3

Lg14

white

met

melanoid

Salamander Genome

slide12

Candidate Genes

sex

Cross-Referencing

melanoid

white

met

slide13

Primary Mechanism of Duplication : Unequal Crossing Over

Crossing over

Between Daughter

Strands

Addition (duplication)

Deletion

(tandom duplications)

Crossing over

Between Daughter

Strands

Addition

Deletion

concerted evolution
Concerted Evolution
  • Members of a gene family evolve in concert.
    • Mutations are transferred among members of the family (homogenization)
    • Mutations are spread to all individuals in the population (fixation).
slide15

Fate of Duplicated Loci

  • Both copies retain original function

e.g. rRNA genes

(2) Gain new function through mutation and selection

e.g. globin genes

(3) Become functionless pseudogenes

e.g globin genes

slide16

a

Duplication

TD

a

b

Speciation

TS

a

b

a

b

Species 2

Species 1

aandbare said to be paralogous genes

aspecies1andaspecies2are said to be orthologous genes

slide17

Time of duplication may be estimated by observing the

phylogenetic distribution of genes

All vertebrates but jawless fish have a and b

H1: Two independent gene losses

H2: Duplication

slide18

Processed

Pseudogene

Creation of a processed pseudogene.

fate of a processed pseudogene
Fate of a Processed Pseudogene
  • Functional

Jingwei (see your book, p. 464)

Human phosphoglycerate kinase (PGK)

Preproinsulin in some mammals

  • Nonfunctional
    • Examples are known for all gene types
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