Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes.
BACKGROUND
Roo is the most abundant retrotransposon in the fruit fly Drosophila melanogaster. Its evolutionary origins and dynamics are thus of special interest for understanding the evolutionary history of Drosophila genome organization. We here study the phylogenetic distribution and evolution of roo, and its highly diverged relative rooA in 12 completely sequenced genomes of the genus Drosophila.


RESULTS
We identify a total of 164 roo copies, 57 of which were previously unidentified copies that occur in 9 of the 12 genomes. Additionally we find 66 rooA copies in four genomes and remnants of this element in two additional genomes. We further increased the number of elements by searching for individual roo/rooA sequence domains. Most of our roo and rooA elements have been recently inserted. Most elements within a genome are highly similar. A comparison of the phylogenetic tree of our roo and rooA elements shows that the split between roo and rooA took place early in Drosophila evolution. Furthermore there is one incongruency between the species tree and the phylogenetic tree of the roo element. This incongruency regards the placement of elements from D. mojavensis, which are more closely related to D. melanogaster than elements from D. willistoni.


CONCLUSIONS
Within genomes, the evolutionary dynamics of roo and rooA range from recent transpositional activity to slow decay and extinction. Among genomes, the balance of phylogenetic evidence, sequence divergence distribution, and the occurrence of solo-LTR elements suggests an origin of roo/rooA within the Drosophila clade. We discuss the possibility of a horizontal gene transfer of roo within this clade.
de la Chaux
Nicole
N
Department of Biochemistry, University of Zurich, Zurich, Switzerland. n.delachaux@bioc.uzh.ch
Wagner
Andreas
A
D000818:Animals; D004330:Drosophila / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D049750:Genome, Insect; D018626:Retroelements; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D018626:Retroelements
Dev Biol. 1999 Feb 15;206(2):178-88
9986731
Trends Genet. 1997 Aug;13(8):335-40
9260521
Nature. 1994 Sep 15;371(6494):215-20
8078581
Trends Genet. 2004 Jul;20(7):314-9
15219396
Mol Biol Evol. 2007 Aug;24(8):1586-91
17483113
Genome Res. 2005 Feb;15(2):330-40
15687296
Nat Genet. 1999 Feb;21(2):209-12
9988275
Gene. 2008 Mar 31;411(1-2):87-93
18281162
Cell. 1982 Jan;28(1):165-76
6279311
Mol Biol Evol. 1999 Sep;16(9):1251-5
10486980
Trends Genet. 2004 Sep;20(9):417-23
15313550
FEMS Microbiol Lett. 2002 Nov 5;216(2):133-8
12435493
Science. 2008 Jun 20;320(5883):1632-5
18566285
J Hum Genet. 1998;43(2):77-84
9621510
J Mol Biol. 1982 May 25;157(3):435-51
6181263
Genetica. 2002 May;115(1):29-36
12188046
Proc Natl Acad Sci U S A. 1982 Sep;79(18):5621-5
6291054
Gene. 2001 Jan 24;263(1-2):219-30
11223261
Nat Genet. 1998 Sep;20(1):43-5
9731528
J Mol Biol. 2000 Sep 8;302(1):205-17
10964570
Trends Genet. 2000 Jun;16(6):276-7
10827456
Gene. 2005 Sep 12;357(2):115-21
16102916
Heredity (Edinb). 2005 Mar;94(3):280-94
15674378
Genome Res. 2001 Sep;11(9):1527-40
11544196
Nature. 2007 Nov 8;450(7167):203-18
17994087
Genome Biol. 2002;3(12):RESEARCH0084
12537573
J Mol Biol. 1994 Feb 4;235(5):1501-31
8107089
Syst Biol. 2003 Oct;52(5):696-704
14530136
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51
16381856
Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8
18039703
Mol Genet Genomics. 2008 May;279(5):463-72
18253751
J Mol Evol. 1998 Jul;47(1):14-20
9664692
Genome Biol. 2009 Feb 18;10(2):R22
19226459
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Nucleic Acids Res. 2007;35(16):5284-93
17686783
Genetica. 2002 May;115(1):81-91
12188050
Trends Genet. 2005 Apr;21(4):200-3
15797612
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
7984417
Genetica. 1999;105(1):43-62
10483093
Syst Biol. 2006 Aug;55(4):539-52
16785212
J Mol Evol. 2000 Jan;50(1):1-10
10654254
Genetics. 1991 Dec;129(4):1085-98
1783293
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
15034147
Nucleic Acids Res. 2005 Jan 20;33(2):511-8
15661851
Genome Res. 2003 Aug;13(8):1889-96
12869581