New Drosophila P-like elements and reclassification of Drosophila P-elements subfamilies

Abstract

Genomic searches for P-like transposable elements were performed (1) in silico in the 12 available Drosophila genomes and (2) by PCR using degenerate primers in 21 Neotropical Drosophila species. In silico searches revealed P-like sequences only in Drosophila persimilis and Drosophila willistoni. Sixteen new P-like elements were obtained by PCR. These sequences were added to sequences of previously described P-like elements, and a phylogenetic analysis was performed. The subfamilies of P-elements described in the literature (Canonical, M, O, T, and K) were included in the reconstructed tree, and all were monophyletic. However, we suggest that some subfamilies can be enlarged, other subdivided, and some new subfamilies may be proposed, totalizing eleven subfamilies, most of which contain new P-like sequences. Our analyses support the monophyly of P-like elements in Drosophilidae. We suggest that, once these elements need host-specific factors to be mobilizable, the horizontal transfer (HT) of P-like elements may be inhibited among more distant taxa. Nevertheless, HT among Drosophilidae species appears to be a common phenomenon.

A Divergent P Element and Its Associated MITE, BuT5, Generate Chromosomal Inversions and Are Widespread within the Drosophila repleta Species Group

“…7) indicate that it should be placed in this family rather than in the other two closely related families ( 1360 and Galileo ) of the P superfamily. This finding suggests that P elements may be more widespread within the Drosophila genus than previously thought and have gone undetected in previous bioinformatic or experimental searches due to their divergence from canonical D. melanogaster P element (Loreto et al 2012). …”

“…To place our D. buzzatii P element in the context of other P elements from Drosophila and other Dipterans, an alignment was made with the nucleotide sequences of the P -element fragments generated by Clark and Kidwell (1997) and Loreto et al (2012). The nucleotide identity between our P element and those previously isolated from Drosophila , Scaptomyza, Lordiphosa, and Lucilia genera is very low, and the alignment was not very reliable.…”

“…For instance, the human genome contains 12 THAP-domain containing genes, and one of them (THAP9) has been recently shown to encode an active P -element transposase (Majumdar et al 2013). In Drosophila , P element is widespread within the Sophophora subgenus (Daniels et al 1990; Hagemann et al 1992, 1994, 1996a, 1996b; Clark and Kidwell 1997) but seems much more scarce in the Drosophila subgenus (Loreto et al 2001, 2012). An almost complete copy was isolated from D. mediopunctata in the tripunctata species group (Loreto et al 2001), whereas relatively short fragments have been amplified by polymerase chain reaction (PCR) in other species of the tripunctata and cardini species groups (Loreto et al 2012).…”

“…In Drosophila , P element is widespread within the Sophophora subgenus (Daniels et al 1990; Hagemann et al 1992, 1994, 1996a, 1996b; Clark and Kidwell 1997) but seems much more scarce in the Drosophila subgenus (Loreto et al 2001, 2012). An almost complete copy was isolated from D. mediopunctata in the tripunctata species group (Loreto et al 2001), whereas relatively short fragments have been amplified by polymerase chain reaction (PCR) in other species of the tripunctata and cardini species groups (Loreto et al 2012). The D. mediopunctata P element is 96.5% identical to that of D. melanogaster, and it has been suggested that it is the result of a horizontal transfer event (Loreto et al 2001).…”

Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome

“…The presence of Galileo subfamilies within the same genome seems to be the rule rather than the exception, as was previously found in D. buzzatii (subfamilies G, K, and N), D. virilis (subfamilies A and B), and D. mojavensis (subfamilies C, D, E, F, and X) [6–8]. Furthermore, the coexistence of different subfamilies, subgroups, or variants of TEs was reported in studies of Bari [37] and G ypsy [38] in Drosophila , P in Anopheles gambiae and Drosophila [39, 40], and mariner in insects and humans [41, 42], among others.…”