1. Comparison of Drosophila Genomes Li-Lun, Ho

2. 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)

3. 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.

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

5. 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.

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

7. 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. significant in DNA recombination. 3. If there is any correlation, what factor affects DNA recombination rate more? (position, number, type of transposable elements)

8. Retrotransposon gene trees of D. melanogaster and D. yakuba Mol. Bio. Evo. 21(9): 1620-1624, 2004

9. THARE Location in D. melanogaster chromosome 2L Mol. Bio. Evo. 21(9): 1620-1624, 2004

10. Number of Retrieved Copies of the D. melanogaster Transposable Elements Analyzed Genome Res. 12: 400-407, 2002

11. Correlation between Transposable Element and Recombination Rate in D. melanogaster genome Genome Res. 12: 400-407, 2002 LTR retrotransposons Non-LTR retrotransposons Transposons TE densities

12. 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.

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

14. Comparison 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 1122223 1,000,001 1204000 2,000,001 1011014 3,000,001 1131223 4,000,001 541223 5,000,001 532103 6,000,001 500010 7,000,001 361020 8,000,001 1252105 9,000,001 423002 10,000,001 813012 11,000,001 931307 12,000,001 1315071

15. 13,000,001 636020 14,000,001 713107 15,000,001 1200161 16,000,001 611035 17,000,001 6440122 18,000,001 244005 19,000,001 13053314 20,000,001 301333238 21,000,001 222710614 22,000,001 4763813 total 21679682898132

16. Distribution of transposable elements in D. melanogaster and D. yakuba Telomeric region Centromeric region

17. Distribution of transposable elements in D. melanogaster and D. yakuba Telomeric region Centromeric region

18. Distribution of transposable elements in D. melanogaster and D. yakuba Telomeric region Centromeric region

19. TART Element Distribution From UCSC genome website

20. Detection of Recombination within Telomeric region of Chromosome 2L

21. Methodology of TOPALi Mol. Bio. Evo. 20(3): 315-337, 2003

22. Detection of DNA Recombination Rate

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

24. Evolutionary Species Tree

25. Trees Generated by TOPALi DSS 95000-190000 DSS 1-190000 DSS 95000-190000 HMM 1-190000HMM 95000-190000HMM 1-95000

26. Trees derived from TOPALi DSS 100,000-150,000 DSS 150,000-190,000

27. Trees derived from TOPALi DSS 1-40000

28. Mosaic Structures TOPALi can not create mosaic structure diagram on the data set. TOPALi can not create mosaic structure diagram on the data set.

29. 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.

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

31. Acknowledgement Dr. Webb Miller Dr. Webb Miller Dr. Claude dePamphilis Dr. Claude dePamphilis