Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside

Abstract

The recent release of the complete euchromatic genome sequence of Drosophila melanogaster offers a unique opportunity to explore the evolutionary history of transposable elements (TEs) within the genome of a higher eukaryote. In this report, we describe the annotation and phylogenetic comparison of 178 full-length long terminal repeat (LTR) retrotransposons from the sequenced component of the D. melanogaster genome. We report the characterization of 17 LTR retrotransposon families described previously and five newly discovered element families. Phylogenetically, these families can be divided into three distinct lineages that consist of members from the canonical Copia and Gypsy groups as well as a newly discovered third group containing BEL, mazi, and roo elements. Each family consists of members with average pairwise identities > or =99% at the nucleotide level, indicating they may be the products of recent transposition events. Consistent with the recent transposition hypothesis, we found that 70% (125/178) of the elements (across all families) have identical intra-element LTRs. Using the synonymous substitution rate that has been calculated previously for Drosophila (.016 substitutions per site per million years) and the intra-element LTR divergence calculated here, the average age of the remaining 30% (53/178) of the elements was found to be 137,000 +/-89,000 yr. Collectively, these results indicate that many full-length LTR retrotransposons present in the D. melanogaster genome have transposed well after this species diverged from its closest relative Drosophila simulans, 2.3 +/-.3 million years ago.

Figure 1

Neighbor-joining phylogenetic tree of the ClustalW alignment of LTR retrotransposon nucleotide sequences. This tree indicates the high level of sequence homology within a family of elements. For clarity, the element families are listed once with the number of elements in each family in parentheses. Unclassified elements are identified by the accession number in which they are located.

Figure 2

(A) Amino-acid alignment of the RT motif of Drosophila melanogaster LTR retrotransposons found in this study. The sequences were aligned using ClustalX as described in Methods. The seven conserved domains of RT (Xiong and Eickbush 1988) are indicated above the alignment. Residue coloring was performed by MacBoxshade v2.01 and is based on the similarity scheme (F, W, Y), (I, L, M, V), (P), (D, E), (G, A), (S, T, C), (N, H), (R, K), (Q). Members of a similar residue group are shaded identically. (B) Unrooted neighbor joining tree of sequences shown in A. Numbers found adjacent to branches indicate bootstrap support from 100 replicates. (C) Neighbor joining phylogenetic tree of the alignment shown in Arooted with the branch leading to the 1731 and copia lineages. Branches with bootstrap values <50 were collapsed to indicate only well-supported groups. Novel element families first characterized in this study are in boldface type and indicated by asterisks.

Figure 2

(A) Amino-acid alignment of the RT motif of Drosophila melanogaster LTR retrotransposons found in this study. The sequences were aligned using ClustalX as described in Methods. The seven conserved domains of RT (Xiong and Eickbush 1988) are indicated above the alignment. Residue coloring was performed by MacBoxshade v2.01 and is based on the similarity scheme (F, W, Y), (I, L, M, V), (P), (D, E), (G, A), (S, T, C), (N, H), (R, K), (Q). Members of a similar residue group are shaded identically. (B) Unrooted neighbor joining tree of sequences shown in A. Numbers found adjacent to branches indicate bootstrap support from 100 replicates. (C) Neighbor joining phylogenetic tree of the alignment shown in Arooted with the branch leading to the 1731 and copia lineages. Branches with bootstrap values <50 were collapsed to indicate only well-supported groups. Novel element families first characterized in this study are in boldface type and indicated by asterisks.

Figure 2

(A) Amino-acid alignment of the RT motif of Drosophila melanogaster LTR retrotransposons found in this study. The sequences were aligned using ClustalX as described in Methods. The seven conserved domains of RT (Xiong and Eickbush 1988) are indicated above the alignment. Residue coloring was performed by MacBoxshade v2.01 and is based on the similarity scheme (F, W, Y), (I, L, M, V), (P), (D, E), (G, A), (S, T, C), (N, H), (R, K), (Q). Members of a similar residue group are shaded identically. (B) Unrooted neighbor joining tree of sequences shown in A. Numbers found adjacent to branches indicate bootstrap support from 100 replicates. (C) Neighbor joining phylogenetic tree of the alignment shown in Arooted with the branch leading to the 1731 and copia lineages. Branches with bootstrap values <50 were collapsed to indicate only well-supported groups. Novel element families first characterized in this study are in boldface type and indicated by asterisks.

Figure 3

Unrooted neighbor joining phylogram of the nucleotide alignments of the HMS Beagle elements. Bootstrap values are shown on branches. The age of the individual elements as calculated by LTR sequence divergence is shown in parentheses following the name of the individual elements.

Figure 4

Translation of roo reveals one long ORF. The characteristic amino acid motifs of Gag, Protease, RT, Ribonuclease H (Rnase H), and Integrase of LTR retrotransposons and retroviruses (McClure 1991) are shaded and labeled in the margin. The region containing motifs similar to other Envelope proteins (Lerat and Capy 1999) is indicated near the end of the ORF.

Figure 5

(A) Graph of LTR retrotransposon element ages of those elements that contain LTR nucleotide divergence values other than zero. (B) Graph of LTR retrotransposon family ages based on average pairwise identities of elements contained within a single family. The number of elements is shown in parentheses following the family name. Error bars indicate standard deviation of ages.

Figure 5

(A) Graph of LTR retrotransposon element ages of those elements that contain LTR nucleotide divergence values other than zero. (B) Graph of LTR retrotransposon family ages based on average pairwise identities of elements contained within a single family. The number of elements is shown in parentheses following the family name. Error bars indicate standard deviation of ages.