Comparison of Drosophila Genomes

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Comparison of Drosophila Genomes

• Li-Lun, Ho

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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)
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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.
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Homology of Retrotransposon
Mol. Bio. Evo. 21(9) 1620-1624, 2004.
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• 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.

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Telomere Structures
Annu. Rev. Genet. 2003. 37485511
Genome Biology 3(10) 1-7, 2002
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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)

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Retrotransposon gene trees of D. melanogaster and
D. yakuba
Mol. Bio. Evo. 21(9) 1620-1624, 2004
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THARE Location in D. melanogaster chromosome 2L
Mol. Bio. Evo. 21(9) 1620-1624, 2004
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Number of Retrieved Copies of the D. melanogaster
Transposable Elements Analyzed
Genome Res. 12 400-407, 2002
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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
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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.

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Density of LTR Retrotransposons according to the
recombination rate on different chromosomes in D.
melanogaster
Genome Res. 12 400-407, 2002

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Comparison of Numbers of Transposon in D.
melanogaster and D. yakuba
LTR retrotransponsons LTR retrotransponsons Non-LTR retrotransponsons Non-LTR retrotransponsons transponson transponson
Chromosome 2L D .meglanogaster D.yakuba D.meglanogaster D.yakuba 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
15
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

total 216 79 68 28 98 132
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Distribution of transposable elements in D.
melanogaster and D. yakuba
Telomeric region
Centromeric region
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Distribution of transposable elements in D.
melanogaster and D. yakuba
Telomeric region
Centromeric region
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Distribution of transposable elements in D.
melanogaster and D. yakuba
Telomeric region
Centromeric region
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TART Element Distribution
From UCSC genome website
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Detection of Recombination within Telomeric
region of Chromosome 2L
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Methodology of TOPALi
Mol. Bio. Evo. 20(3) 315-337, 2003
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Detection of DNA Recombination Rate
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• Can I find some sequences within telomeric
  regions which can build up a gene tree closer to
  species tree?

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Evolutionary Species Tree
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Trees Generated by TOPALi
DSS 1-190000
DSS 95000-190000
DSS 95000-190000
HMM 1-190000
HMM 95000-190000
HMM 1-95000
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Trees derived from TOPALi
DSS 150,000-190,000
DSS 100,000-150,000
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Trees derived from TOPALi
DSS 1-40000
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Mosaic Structures

• TOPALi can not create mosaic structure diagram on
  the data set.

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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.
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Possible Alternative Method
1. PDM (Probabilistic divergence measure).
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Acknowledgement

• Dr. Webb Miller
• Dr. Claude dePamphilis

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