Comparison of Drosophila Genomes
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Transcript of Comparison of Drosophila Genomes
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