Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes

Abstract

The techniques that are usually used to detect transposable elements (TEs) in nucleic acid sequences rely on sequence similarity with previously characterized elements. However, these methods are likely to miss many elements in various organisms. We tested two strategies for the detection of unknown elements. The first, which we call "TBLASTX strategy," searches for TE sequences by comparing the six-frame translations of the nucleic acid sequences of known TEs with the genomic sequence of interest. The second, "repeat-based strategy," searches genomic sequences for long repeats and clusters them in groups of similar sequences. TE copies from a given family are expected to cluster together. We tested the Drosophila melanogaster genomic sequence and the recently sequenced Anopheles gambiae genome in which most TEs remain unknown. We showed that the "TBLASTX strategy" is very efficient as it detected at least 332 new TE families in D. melanogaster and 400 in A. gambiae. This was unexpected in Drosophila as TEs of this organism have been extensively studied. The "repeat-based strategy" appeared to be very inefficient because of two problems: (i) TE copies are heavily deleted and few copies share homologous regions, and (ii) segmental duplications are frequent and it is not easy to distinguish them from TE copies.

THAP5 is a human cardiac-specific inhibitor of cell cycle that is cleaved by the proapoptotic Omi/HtrA2 protease during cell death

“…The closest orthologs were detected in Macaca fascicularis, Bos taurus, and Gallus gallus. The absence of orthologs in mouse and rat has also been reported for four other members of the THAP family, the THAP6, THAP8, THAP9, and THAP10 proteins (37). It was suggested that some THAP genes might have originated from a domestication event of a single copy of P element transposase that took place in the human lineage after it had diverged from the rodent lineage (38).…”

Population Genetics Models of Competition Between Transposable Element Subfamilies

“…Others, such as Plasmodium and other protista parasites, show only very mutated TE-derived sequences or no recognizable TE at all (Gardner et al 2002). On the other hand, D. melanogaster has many active elements and even more inactive elements (Bartolomé et al 2002), sometimes from families with no corresponding active copy in this genome (Quesneville et al 2003). H. sapiens has a huge number of TE sequences, but very few of them are potentially active (Lander et al 2001).…”

A model of segmental duplication formation in Drosophila melanogaster

“…The method can be briefly sketched as follows (see Methods). First, we detected all repeated sequences in the genome with the BLASTER program using BLASTN repeatedly in an all-by-all genome comparison (Altschul et al 1990(Altschul et al , 1997Quesneville et al 2003Quesneville et al , 2005. Second, to specifically detect repeats generated by a duplication process, we filtered out repetitive DNAs generated by other processes (Fig.…”

“…1). Therefore, we were able to eliminate all detected repeated sequences that did not correspond to a SD copy (i.e., TEs or microsatellites), using TE annotations of the D. melanogaster Release 4 genome (Quesneville et al 2003(Quesneville et al , 2005 and microsatellite annotations detected with the TRF program (Benson 1999) (see Methods). To be more stringent, we also used annotations of potential new TEs detected by BLASTER with TBLASTX (Altschul et al 1990(Altschul et al , 1997Quesneville et al 2003Quesneville et al , 2005) and a compilation of known eukaryotic TEs (Repbase Update Release 8.12; Jurka 2000).…”