Comparison of
Drosophila Genomes
Li-Lun, Ho
D. melanogaster vs. D. yakuba
D. yakuba genome is assembled
in Apr, 2004.
D. yakuba genome has 14 times
higher recombination rate than
D. melanogaster in the telomeric
region of the X chromosome.
The result indicates a relaxation of
purifying selection of deleterious
mutation in the melanogaster lineage
and a manifestation of positive selection
in the yakuba lineage.
(Genetics 153: 1285-1296, 1999)
(Begun et.al., 2004)
The Relationships between DNA Recombination and
Telomeres
1.The reduction of recombination rates in the telomeric regions of D.
melanogaster results in the reduction of the selection efficacy.
(Genetics 153: 1285-1296, 1999)
2. The D. melanogaster 2L chromosome has 22, 217,913 base pairs and
the D. yakuba 2L chromosome has 22,678,881 base pairs.
3. Drosophila telomeres break the some cardinal rules of telomeres.
(Genome Biology 3(10) 1-7, 2002.)
a. Telomere maintenance in Drosophila is not performed by the
canonical telomerase (primary end protection or capping
function) but by a unique transposition mechanism.
b. Two non LTR retrotransposable elements, HeT-A and TART
telomere associated retrotransposons, are specifically located at
the end of chromosomes.
Homology of Retrotransposon
Mol. Bio. Evo. 21(9): 1620-1624, 2004.
c. Truncated Drosophila telomeres can be maintained and
passed on both somatically and through the germ line, despite
their progressive erosion over generations in the absence of
HeT-A or TART element.
4. TART and HeT-A elements have been performing the cellular
function of telomere maintenance for more than 60 million years.
Mol. Bio. Evo. 21(9): 1620-1624, 2004.
a. The evolutionary origin of telomeric retrotransposons remains
controversial. However, it has been suggested that the common
features of these elements result from the convergent evolution
but not from evolution from a common ancestor.
b.TAHRE, a novel telomeric retrotransposon from Drosophila
melanogaster, reveals the origin of Drosophila telomerase.
Telomere Structures
Genome Biology 3(10) 1-7, 2002
Annu. Rev. Genet. 2003. 37:485–511
Aim
1. To find out if there is any correlation between
transposable element and recombination rate of
D. melanogaster and D. yakuba chromosome 2L.
2. To find out which transposable element is more
significant in DNA recombination.
3. If there is any correlation, what factor affects
DNA recombination rate more? (position,
number, type of transposable elements)
Retrotransposon gene trees of D. melanogaster and D. yakuba
Mol. Bio. Evo. 21(9): 1620-1624, 2004
THARE Location in D. melanogaster
chromosome 2L
Mol. Bio. Evo. 21(9): 1620-1624, 2004
Number of Retrieved Copies of the D. melanogaster
Transposable Elements Analyzed
Genome Res. 12: 400-407, 2002
Correlation between Transposable Element and
Recombination Rate in D. melanogaster genome
Genome Res. 12: 400-407, 2002
LTR retrotransposons
Non-LTR retrotransposons
TE densities
Transposons
Results from Previous Studies


The density of LTR and non-LTR
retrotransposons was high in regions
with low recombination rates.
The density of transposons was
significantly negatively correlated with
recombination rates.
Density of LTR Retrotransposons according to the recombination
rate on different chromosomes in D. melanogaster
Genome Res. 12: 400-407, 2002
Comparison of Numbers of Transposon in D. melanogaster and D. yakuba
LTR retrotransponsons
Chromosome 2L
D .meglanogaster
Non-LTR retrotransponsons
D.yakuba
D.meglanogaster
D.yakuba
transponson
D.meglanogaster
D.yakuba
1
11
2
2
2
2
3
1,000,001
12
0
4
0
0
0
2,000,001
10
1
1
0
1
4
3,000,001
11
3
1
2
2
3
4,000,001
5
4
1
2
2
3
5,000,001
5
3
2
1
0
3
6,000,001
5
0
0
0
1
0
7,000,001
3
6
1
0
2
0
8,000,001
12
5
2
1
0
5
9,000,001
4
2
3
0
0
2
10,000,001
8
1
3
0
1
2
11,000,001
9
3
1
3
0
7
12,000,001
13
1
5
0
7
1
total
13,000,001
6
3
6
0
2
0
14,000,001
7
1
3
1
0
7
15,000,001
12
0
0
1
6
1
16,000,001
6
1
1
0
3
5
17,000,001
6
4
4
0
12
2
18,000,001
2
4
4
0
0
5
19,000,001
13
0
5
3
3
14
20,000,001
30
1
3
3
32
38
21,000,001
22
27
10
6
14
14
22,000,001
4
7
6
3
8
13
216
79
68
28
98
132
Distribution of transposable elements in D. melanogaster
and D. yakuba
LTR Retrotransposon Distribution on Chromosome 2L in
Drosophila
35
copy numbers
30
25
20
D. melanogaster
15
D. yakuba
10
5
0
1
3
5
7 9 11 13 15 17 19 21 23
nucleotides (x1000)
Telomeric region
Centromeric region
Distribution of transposable elements in D. melanogaster
and D. yakuba
Non-LTR Retrotransposons Distribution on Chromosome 2L
in Drosophila
copy numbers
12
10
8
D.melanogaster
D. yakuba
6
4
2
0
1
3
5
Telomeric region
7 9 11 13 15 17 19 21 23
nucleotides (x1000)
Centromeric region
Distribution of transposable elements in D. melanogaster
and D. yakuba
Transposon Distribution on Chromosome 2L in
Drosophila
copy numbers
40
30
D.melanogaster
D.yakuba
20
10
0
1 3 5 7 9 11 13 15 17 19 21 23
nucleotides (x1000)
Telomeric region
Centromeric region
TART Element Distribution
From UCSC genome website
Detection of Recombination within Telomeric
region of Chromosome 2L
Methodology of TOPALi
Mol. Bio. Evo. 20(3): 315-337, 2003
Detection of DNA Recombination Rate

Can I find some sequences within
telomeric regions which can build up
a gene tree closer to species tree?
Evolutionary Species Tree
Trees Generated by TOPALi
DSS 1-190000
HMM 1-190000
DSS 95000-190000
HMM 1-95000
DSS 95000-190000
HMM 95000-190000
Trees derived from TOPALi
DSS 100,000-150,000
DSS 150,000-190,000
Trees derived from TOPALi
DSS 1-40000
Mosaic Structures

TOPALi can not create mosaic
structure diagram on the data set.
Conclusions
1. The intron length may also affect recombination
rate of chromosome.
2. The scanning window should be adjusted either
longer or shorter region on the chromosome.
3. The telomeric region of other long chromosomes
(2L, 3L, 3R) should be examined to verify the
the correlations between DNA recombination rate
and transposable element.
4. The chromosome recombination rate map of D.
yakuba needs to be built up.
Possible Alternative Method
1. PDM (Probabilistic divergence measure).
Acknowledgement


Dr. Webb Miller
Dr. Claude dePamphilis