EE Lecture 10: Genome Evolution Flashcards
1
Q
what is the C value paradox
A
lower end of organisms gene numbers correlates with complexity
2
Q
what is the c value
A
the total amount of DNA in the haploid genome
3
Q
what explains C-value paradox
A
non coeding DNA
4
Q
how does amount of non coding DNA change
A
transposition replication slippage unequal crossing over polyploidy chomosomal duplicationq
5
Q
what are the processes behind changes in genome size in genic regionsq
A
gene duplication and loss
6
Q
what are the processes behind changes in genome size in nongenic regions
A
selfish DNA
7
Q
what are multigene families
A
groups of genes from same organism that encode protein with simillar sequences either over their full length or limited to a specific domain
can be tandemly repeated or dispersed in gene clusters
8
Q
give an example of a gene family
A
globin gene
9
Q
what does the multigene globin family allow for
A
the production of different types of Hb; embryonic, fetal, adult
10
Q
how did Globins arise
A
from a single origin 800MYA
then series of gene duplications due to unequal cross over, followed by mutation and divergence in function
11
Q
how did rDNA evolve
A
by gene duplication but also concerted evoln to produce lots of ribosomes with the same function
12
Q
what is concerted evoln
A
explains the observation that paralogs are more closely related than orthologs
13
Q
what are paralogs
A
genes related by duplication in a genome
14
Q
what is concerted evoln caused by
A
gene conversion
the DNA sequence of one gene is replaced by the DNA sequence from another
15
Q
what are homologs
A
2 genes related by common ancestry
16
Q
what are orthologs
A
genes in different species that evolved from common ancestral gene by speciation - normally retain same function
17
Q
what explains the observation that paralogs are more closely ewlated than orthologs
A
concerted evoln
18
Q
what are 2 genes related by common ancestry called
A
homologs
19
Q
what are genes in different species that have evolved from common ancestral gene by speciation called
A
orthologs
20
Q
what are 2 genes that have evolved by duplication called
A
paralogs
21
Q
which retain same function, orthologs or paralogs
A
orthologs
22
Q
what evoln is caused by gene conversion
A
concerted evoln
23
Q
how common is gene duplication
A
relatively common
0.01/gene/MYrs
24
Q
what is the outcome of most gene duplicates
A
theyre lost or silenced, few can survive and diverge to new functions or maintain same function (dosage or regulation)
25
what is normal transmission rate of meiosis
d = 0.5
26
why are selfish genetic elements selfish
because they bias their transmission to become rapidly fixed in popns
27
how is inheritance bias caused
gonotaxis
interference
overreplication
28
under what circumstances would SGEs (selfish genetic elements) not become rapidly fixed in popns
if opposed by evolnary forces
29
what are examples of SGEs
chromosomes
genes
haplotypes
cytoplasmic factors like Wolbachia bacteria
30
what is Wolbachia bacteria an example of
a selfish genetic element
31
what is gonotaxis
orientating towards the germ line
32
what is interference
aggressive competition to get in germline
33
over-replication
replicating more than once during the cell cycle
34
give an example of inheritance bias caused by gonotaxis
Gonotaxis of B chromosomes
35
in what percentage of plants does gonotaxis of B chromosomes occur
10-15%plant and animal species and fungi
36
what are B chromosomes
genetic element that employs gonotaxis
found in the nucleus and rarely coding (unlike A chroms)
they avoid undergoing proper cell division and and seek to enter germline in as large numbers as possible
37
are B chroms essential, where do they originate from
no, supernumary - not all individuals possess them
| they originate from A set (sex chroms)
38
how many B chroms do chives have in mitotic metaphase
3
39
how many B chroms do Myrmeleotettix maculatus GRASSHOPPER have in mitotic metaphase
2
40
what percentage of individuals in Britain have B chroms
50%
41
what is transmission rate of B chroms - down which lineage?
inherited through females
| d=0.8
42
discuss fitness efrfects in grasshoppers
2B and above = very unfit
slows development from diapause to adult
causes sperm dysfunction
43
what can having 2Bs and above cause
slow development from diapause to adult
| sperm dysfunction
44
why are B chroms seen as genomic parasites
theyre detrimental to their carriers by reducing fitness
45
what does the parasitic model of B chrom evoln show
stable frequencies of B chrom gonotaxis maintained due to an eqbm between B chrom accumulation and deleterious effects of B chrom on its carriers
46
how is inheritance bias caused by over-replication
increased rate transmission due to being copied more than once during cell cycle
47
where does inheritance bias caused by over replication occur
in germ line and somatic cell
48
how often do transposable elements transpose
NOT every cell generation
49
name some types of transposable elements
DNA transposons
RNA elements :
NON-LTR retrotransposons -LINEs&SINEs
LTR retroelements:endogenous retroviruses-in humans
50
what are RNA elements divided into
NON-LTR retrotransposons
| LOT retroelements inc.LTR retrotransposons (not in humans) and Endogenous Retroviruses (in humans)
51
how much of human genome % is made of DNA transposons
3%
52
how much of humans DNA is made of selfish genetic elements
46%`
53
what constitute Non-LTR retrotransposons
LINEs
| SINEs
54
what are LINEs/SINEs
Long Interspersed Nuclear Elements
55
in what form in DNA do transposable elements generally exist
epigenetically silenced form
eg. through DNA methylation
histone modification
RNA directed DNA methylation
56
name some ways of epigenetically silencing
DNA methylation
histone modification
RNA directed DNA methylation
57
what are DNA transposons
transposable elements:
| DNA sequences that are able to move from one location to another via copy paste mechanisms
58
how long are DNA transposon sequences
1-19kb long
59
what mechanism do DNA transposons use
cut and paste mechanism
60
how many gene products do DNA transposons produce
a single transposase product
61
outline the mechanism for DNA transposons
1. transposase binds to donor DNA
2. formation of a paired end complex with a monomer of Tn10 transposase bound to each end
3. Transposase cuts donor and target DNA
4. Dbl stranded cleavage of donor DNA at both ends of transposase DNA complex (DNA remains supercoiled)
5. Staggered cuts in target DNA
6. Each strand of donor DNA is covalently joined to target DNA
7. Staggered cuts are filled in by DNAP1, this explains the target site duplication
62
what can transposable element mobilization promote
gene inactivation
gene expression
induce illegitimate recombination
63
how can TEs inactivate/alter the expression of genes
insertion with introns, exons or regulatory genes
64
give examples of Non-LTR retrotransposons
LINEs
| SINEs
65
give examples of LTR retroelements
```
LTR Retrotransposons -not in humans
Endogenous Retroviruses (in humans)
```
66
which LTR retroelemenrs are in humans
endogenous retroviruses
67
which LTR retroelements are not in humans
LTR retrotransposons
68
what forms when a DNA transposase binds to donor DNA
formation of a "paired end" complex with a monomer of Tn10 transposase bound to each end
69
what is a "paired end complex"
forms when DNA transposase binds to donor DNA, with a monomer of Tn10 transposase bound to each end
70
what is Tn10 involved in
paired end complex - one is bound to each end
71
how are staggered cuts in supercoiled DNA that has been bound to transposase filled
with DNAP1
72
what are retrotransposons
transposons via RNA intermediates
| genetic elements that can amplify themselves in the genome
73
where are retrotransposons particularly abundant
in plants - principle component of nuclear DNA
| in maize, 49-78% genome made up of retrotransposons
74
how much of genome in maize is made up of retrotransposons
49-78%
75
how much of human genome is made up of retrotransposons
42%
76
how do retrotransposons induce mutations
by inserting near/within genes, copying themselves to RNA, then back to DNA that may integrate back into the genome
77
what do retrotransposons encode to enable encoding of DNA
reverse transcriptase
78
what subdivisions of retrotransposons are there
LTR and Non-LTR
79
what does LTR stand for
| what is it
Long Terminal Repeats
| it is a retrotransposon
80
what are the structural domains present in retrotransposons
```
gag - core particle components
en-endonuclease
rt-reverse transcriptase
LTR-Long Terminal Repeat
int-integrase
env-envelope gylcoprotein
```
81
what is gag
a structural domain in retrotransposons that encodes core particle components
82
what is int
structural domain in retrotransposons that encodes integrase
83
what subdivisions of LTR retroelements (of retrotransposons) are there
Ty1-copia
gypsy
retrovirus
84
what is Ty1-copia
a non LTR retrotransposon retrotransposable element
85
what is gypsy group
LTR retrotransposon
86
what is retrovirus
an LTR retrotransposon
87
what structural domains are present in non-LTR retrotransposons
gag - en - rt
88
what structural domains are present in Ty1-copia LTR retrotransposons
LTR - gag - int - rt - LTR
89
what structural domains are present in gypsy LTR retrotransposons
LTR - gag - rt - int - LTR
90
what structural domains are present in retroviruses LTR retroelements
LTR - gag - rt - int - env - LTR
91
what is the following the structure of
| LTR - gag - int - rt - LTR
Ty1-copia LTR Retrotransposon
92
what is the following the structure of
| gag - int - rt
Non - LTR retrotransposons eg. LINEs
93
what is the following the structure of
| LTR - gag - int -rt - LTR
gypsy group retrotransposon
94
what is the following the structure of
| LTR - gag - rt - int - env - LTR
retrovirus
95
what are LTR Retroelements
RNA elements which use reverse transcriptase to make cDNA
96
how many bp long are LTR retroelements
~100bp to >5kb long
97
what are the effects of transposable elements on the host
few are beneficial besides RAG1 and RAG2 genes in immune system
98
outline some beneficial effects of transposable elements on the host
RAG1 and RAG2 immune system
99
outline some neutral effects of transposable elements on the host
variegation in morning glory
100
outline some deleterious effects of transposable elements on the host
P elements in Drosophila cause chromosome breaks
| 0.1-0.2% human disease causing mutations are due to insertion of transposable elements
101
what is RAG1 and RAG2
transposable elements that are beneficial to immune system
102
what are P elements
found in Drosophila and cause chromosome breakage
103
what is the effect of P elements
cause chromosome breaks in drosophila
104
what are 0.1-0.2% of human disease causing mutations due to
insertion of transposable elements
105
discuss the fate of tranposable elements in humans
63 families of extinct DNA transposons (no movement in 50MYRS)
20 families of endogenous retrovirus all invaded in the last 100MYR and almost all inactive
106
how many active transposable elements are in a single individual`
10-100s
107
how many families of extinct DNA transposons are there in humans
63
108
how many families of endogenous retrovius have invaded humans in last 100MYRs, what has happened to them
20 families of endogenous retroviruses have invaded humans in last 100MYRS, all now inative
109
give some examples of adaptive traits
melanic form of peppered moth
| beak size and shape of Darwin's finches
110
what is parallel evoln
the indep evoln of similar traits, starting from a similar ancestral codon
111
give an example of widespread parallel evoln
in sticklebacks - repeateed fixation of Ectodysplasin alleles
112
what allele is involved in stickleback parallel evoln
Ectodysplasin alleles - secreted signalling molecule known to affect scale growth
113
what is Ectodysplasin
allele involved in scale growth - affects sticklebacks in parallel evoln
114
what two types of stickleback forms are there
marine forms: heavily armored
| freshwater forms: lightly armored
115
how are freshwater forms of sticklebacks armored
lightly armored freshwater forms
116
how are marine forms of sticklebacks armored
heavily armored marine forms
117
how many aa changes between the two alleles for heavy/light armor of sticklebacks
marine - heavy Armoured
freshwater - lightly armored
4 aa changes between the 2 alleles
118
how has parallel evoln of stickleback low plated phenotypes @ freshater locations around the world occured
by repeated selection of Ectodysplasin alleles derived from an ancestral low plated haplotype that first appeared >2MYA
119
what methods were used to identify the major chrom locus controlling armor plate patterns in sticklebacks
positional cloning methods
- mapping
- sequencing
- transgenic studies
120
how did EDA trait evolve
EDA low-plated allele evolved once and then spread globally
121
what types of sequencing technologies exist
sanger
454
illumina
122
which sequencing has a readlength of 700BP
pyrosequencing 454
123
```
PYROSEQUENCING 454
Read length
Accuracy
Reads and time per run
+ves
-ves
```
-700BP
-99.9%
1 MILL, 24HRS
long read size, fast
expensive, homopolymer errors
124
```
SEQUENCING MY SYNTHESIS - ILLUMINA
Read length
Accuracy
Reads and time per run
+ves
-ves
```
```
50-300BP
98%
3BILL, 1-10DAYS
Potential high sequence yield
v. expensive, require high [DNA]
```
125
```
CHAIN TERMINATION SANGER
Read length
Accuracy
Reads and time per run
+ves
-ves
```
```
400-900BP
99.9%
NA
20min-3HRS
long individual reads
v useful
more expensive/impractical for larger projects
requires time consuming plasmid cloning
```
126
what are pros&cons of illumina sequencing
potential high sequence yield as 3BILL reads in 1-10days
| BUT v. expensive and require high [DNA]
127
what are pros and cons of 454 Sequencing
99.9% accurate, can read 1 mill in 24hrs
| long read size but expensive and homopolymer errors
128
which type of sequencing can lead to homopolymer errors
454
129
which type of sequencing requires the time consuming plasmid cloning
sanger
130
what are the genes behind beak shape and sinze in finchers
BMP4 bone growing protein: wider heavier
| and Calmodulin:longer and thinner
131
what is the BMP4 gene involved in
bone growing protein; allowing wider and heavier beak size in finches
132
what is Calmodulin gene involved in
longer and thinner beak size in finches
133
what lovus is involved in th e pepered moth
Carbonaria locus
134
what makes us human
bipedal
language
hypoid bone: horseshoe shaped bone -midline neck and chin
135
what is FOXP2 gene
language gene forkhead box protein
136
what do FOXP2 mutations cause
speech and language disorder
137
what happened when FOXp2 mutation was induced in mice
less vocalisation, less exploratory, increased dendrite growth and synaptic plasticity in basal ganglia
better learning ability
138
what happened when FOXp2 mutation was induced in songbirds
inaccurate song
139
which gene is involved in language in humans
FOXP2 forkhead box protein gene
140
who do humans share FOXP2 gene with
NEanderthals
141
who do humans share hyoid bone with
Neanderthals
142
what positively selected genes exist in humans
```
FOXP2
Hyoid bone genes
THADA
genes associated with cognitive ability -schizophrenia, autism
RUNX2
```
143
what is THADA gene associated with
diabetes
| energy metabolism
144
what is RUNX2 associated with
delayed closure of cranial sutures- frontal bone protrusion
145
which positively selected gene is associated diabetes and energy metabolism
THADA
146
what have been the revelations of gene sequencing
1st rev: PCR and DNA sequencing
2nd: next gene whole genome, pop genetics, epigenetics
3rd: make sense of emerging data
