Comparison of Comparison of Drosophila GenomesDrosophila Genomes

Li-Lun, HoLi-Lun, Ho

D. melanogaster vs. D. yakubaD. melanogaster vs. D. yakuba

D. yakuba genome is assembled in Apr, 2004.

D. yakuba genome has 14 times higher recombination rate thanD. melanogaster in the telomericregion of the X chromosome.

The result indicates a relaxation of purifying selection of deleterious mutation in the melanogaster lineage and a manifestation of positive selectionin the yakuba lineage.

(Genetics 153: 1285-1296, 1999)

(Begun et.al., 2004)

The Relationships between DNA Recombination and The Relationships between DNA Recombination and TelomeresTelomeres

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 RetrotransposonHomology 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 StructuresTelomere Structures

Annu. Rev. Genet. 2003. 37:485–511Genome Biology 3(10) 1-7, 2002

AimAim1. To find out if there is any correlation between 1. To find out if there is any correlation between

transposable element and recombination rate of transposable element and recombination rate of D. melanogaster and D. yakuba chromosome D. melanogaster and D. yakuba chromosome 2L.2L.

2. To find out which transposable element is more2. To find out which transposable element is more significant in DNA recombination. significant in DNA recombination.

3. If there is any correlation, what factor affects 3. If there is any correlation, what factor affects DNA recombination rate more? (position, DNA recombination rate more? (position, number, type of transposable elements)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 THARE Location in D. melanogaster chromosome 2Lchromosome 2L Mol. Bio. Evo. 21(9): 1620-1624, 2004

Number of Retrieved Copies of the D. melanogaster Number of Retrieved Copies of the D. melanogaster Transposable Elements Analyzed Transposable Elements Analyzed

Genome Res. 12: 400-407, 2002

Correlation between Transposable Element and Correlation between Transposable Element and Recombination Rate in D. melanogaster genomeRecombination Rate in D. melanogaster genome

Genome Res. 12: 400-407, 2002

LTR retrotransposons

Non-LTR retrotransposons

Transposons

TE densities

Results from Previous StudiesResults 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 Density of LTR Retrotransposons according to the recombination rate on different chromosomes in D. melanogasterrate on different chromosomes in D. melanogaster

Genome Res. 12: 400-407, 2002

Comparison of Numbers of Transposon in D. melanogaster and D. yakubaComparison of Numbers of Transposon in D. melanogaster and D. yakuba LTR retrotransponsons Non-LTR retrotransponsons 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

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

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

LTR Retrotransposon Di stri buti on on Chromosome 2L i nDrosophi l a

05

101520253035

1 3 5 7 9 11 13 15 17 19 21 23nucl eoti des (x1000)

copy numbers

D. mel anogaster

D. yakuba

Telomeric region Centromeric region

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

Non-LTR Retrotransposons Di stri but i on on Chromosome 2Li n Drosophi l a

02468

1012

1 3 5 7 9 11 13 15 17 19 21 23nucl eoti des (x1000)

copy numbers

D. mel anogasterD. yakuba

Telomeric region Centromeric region

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

Transposon Di st r i but i on on Chromosome 2L i nDrosophi l a

0

1020

30

40

1 3 5 7 9 11 13 15 17 19 21 23nucl eot i des (x1000)

copy numbers

D. mel anogasterD. yakuba

Telomeric region Centromeric region

TART Element DistributionTART Element Distribution

From UCSC genome website

Detection of Recombination within Telomeric Detection of Recombination within Telomeric region of Chromosome 2Lregion of Chromosome 2L

Methodology of TOPALiMethodology of TOPALiMol. Bio. Evo. 20(3): 315-337, 2003

Detection of DNA Recombination RateDetection of DNA Recombination Rate

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

Evolutionary Species TreeEvolutionary Species Tree

Trees Generated by TOPALiTrees Generated by TOPALi

DSS 95000-190000DSS 1-190000 DSS 95000-190000

HMM 1-190000 HMM 95000-190000HMM 1-95000

Trees derived from TOPALiTrees derived from TOPALi

DSS 100,000-150,000 DSS 150,000-190,000

Trees derived from TOPALiTrees derived from TOPALi

DSS 1-40000

Mosaic StructuresMosaic Structures TOPALi can not create mosaic TOPALi can not create mosaic

structure diagram on the data set.structure diagram on the data set.

ConclusionsConclusions1. 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 MethodPossible Alternative Method

1. PDM (Probabilistic divergence measure).

AcknowledgementAcknowledgement Dr. Webb MillerDr. Webb Miller Dr. Claude dePamphilisDr. Claude dePamphilis