Losing helena: the extinction of a drosophila line-like element

Abstract

Background: Transposable elements (TEs) are major players in evolution. We know that they play an essential role in genome size determination, but we still have an incomplete understanding of the processes involved in their amplification and elimination from genomes and populations. Taking advantage of differences in the amount and distribution of the Long Interspersed Nuclear Element (LINE), helena in Drosophila melanogaster and D. simulans, we analyzed the DNA sequences of copies of this element in samples of various natural populations of these two species.

Results: In situ hybridization experiments revealed that helena is absent from the chromosome arms of D. melanogaster, while it is present in the chromosome arms of D. simulans, which is an unusual feature for a TE in these species. Molecular analyses showed that the helena sequences detected in D. melanogaster were all deleted copies, which diverged from the canonical element. Natural populations of D. simulans have several copies, a few of them full-length, but most of them internally deleted.

Conclusion: Overall, our data suggest that a mechanism that induces internal deletions in the helena sequences is active in the D. simulans genome.

Figure 1

helena structure. Full-length copy of helena in the D. simulans genome (3R: 1506433 – 15011368). DNA sequence: UTR, untranslated region; ORF, open reading frame; AAA, polyA tail. 5'UTR: ERE, estrogen response element; GATA, SP1, stimulating protein 1; USF-like, upstream stimulating factor-like; Protein sequences: MHR, major homology region; CCHC, cysteine rich domain; AP, apyrimidic. See Materials and Methods for prediction information.

Figure 2

Scheme of helena copies. Representation of helena copies in the D. melanogaster and D. simulans genomes with at least 90% identity and 50% of the length of the complete copy, and with e-values of less than 10e^-10; Triangles = insertions; Spaces = deletions.

Figure 3

Southern blot analysis of D. melanogaster and D. simulans populations. Lanes 1 to 9 are D. melanogaster populations (Bolivia, Brazzaville, Canton, Chicharo, Reunion Island, Arabia, Virasoro, Vietnam, and ISO for the 9^th and 20^th lane). Lanes 1 to 19 are D. simulans populations (Amieu, Eden, Valence, Canberra, Papeete, Moscow, Makindu, Zimbabwe, Cann River and Reunion Island). For both Southern blots, the DNA size is estimated in base pairs.

Figure 4

phylogenetic tree of the DNA sequences from the ORF1 region. The reconstruction was performed on the cloned DNA sequences of the ORF1 region from the different populations of D. simulans, and from some sequences detected in the sequenced genome (we eliminated sequences that were too short relative to the global length of the alignment). Colored boxes identify sequences harboring common patterns of deletions and/or insertions. All the positions are given by reference to the complete copy. Green box: sequences display the same deletions of 118 bp (at position 45), 3 bp (at position 839), 6 bp (at position 846), 1 bp (at position 854) and a 1-bp insertion (at position 415). Blue box: sequences display the same 28-bp deletion (at position 1092) – those with a red star also have a 77-bp deletion (at position 508), and a 91-bp deletion (at position 593). Yellow box: sequences display the same deletions of 1 bp (at position 160), 28 bp (at position 165), 19 bp (at position 954), 2 bp (at position 989), and 37 bp (at position 1006), and an insertion of 1 bp (at position 322). Orange box: sequences with no deletion or insertion, very closely related to the complete copy chr3R_1506433. Black asterisks correspond to bootstrap values greater than 50%.

Figure 5

phylogenetic tree of the DNA sequences from the ORF2 region. The reconstruction was performed on the cloned DNA sequences of the ORF2 region from the different populations of D. simulans and from some sequences detected in the sequenced genome (we eliminated sequences that were too short relative to the global length of the alignment). Colored boxes represent sequences harboring common patterns of deletions and/or insertions. All the positions are given relative to the complete copy. Green box:sequences display the same 4-bp deletion (at position 547) and the same 2-bp insertion (at position 112). Dark blue box: sequences display the same 1-bp deletion (at position 521). Yellow box: sequences display the same deletions of 3 bp (at position 143), 8 bp (at position 335), 4 bp (at position 345), and an insertion of 2 bp (at position 460). Light blue box: sequences display the same 401-bp deletion (at position 179). Orange box: sequences with no deletion or insertion, very closely related to the complete copy chr3R_1506433. Black asterisks correspond to bootstrap values greater than 50%.