Comparison of drosophila genomes
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Comparison of Drosophila Genomes PowerPoint PPT Presentation

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.

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Comparison of Drosophila Genomes

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Comparison of drosophila genomes

Comparison of Drosophila Genomes

Li-Lun, Ho


D melanogaster vs d yakuba

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

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

Homology of Retrotransposon

Mol. Bio. Evo. 21(9): 1620-1624, 2004.


Gudl st

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

Telomere Structures

Genome Biology 3(10) 1-7, 2002

Annu. Rev. Genet. 2003. 37:485–511


Gudl st

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)


Gudl st

Retrotransposon gene trees of D. melanogaster and D. yakuba

Mol. Bio. Evo. 21(9): 1620-1624, 2004


Thare location in d melanogaster chromosome 2l

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

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

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

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.


Gudl st

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

Comparison of Numbers of Transposon in D. melanogaster and D. yakuba


Distribution of transposable elements in d melanogaster and d yakuba

Distribution of transposable elements in D. melanogaster and D. yakuba

Telomeric region Centromeric region


Distribution of transposable elements in d melanogaster and d yakuba1

Distribution of transposable elements in D. melanogaster and D. yakuba

Telomeric region Centromeric region


Distribution of transposable elements in d melanogaster and d yakuba2

Distribution of transposable elements in D. melanogaster and D. yakuba

Telomeric region Centromeric region


Tart element distribution

TART Element Distribution

From UCSC genome website


Detection of recombination within telomeric region of chromosome 2l

Detection of Recombination within Telomeric region of Chromosome 2L


Methodology of topali

Methodology of TOPALi

Mol. Bio. Evo. 20(3): 315-337, 2003


Detection of dna recombination rate

Detection of DNA Recombination Rate


Gudl st

Can I find some sequences within telomeric regions which can build up a gene tree closer to species tree?


Evolutionary species tree

Evolutionary Species Tree


Trees generated by topali

Trees Generated by TOPALi

DSS 1-190000

DSS 95000-190000

DSS 95000-190000

HMM 1-190000

HMM 1-95000

HMM 95000-190000


Trees derived from topali

Trees derived from TOPALi

DSS 150,000-190,000

DSS 100,000-150,000


Trees derived from topali1

Trees derived from TOPALi

DSS 1-40000


Mosaic structures

Mosaic Structures

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


Conclusions

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

Possible Alternative Method

1. PDM (Probabilistic divergence measure).


Acknowledgement

Acknowledgement

  • Dr. Webb Miller

  • Dr. Claude dePamphilis


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