Normal and defective mariner-like elements in Rhynchosciara species (Sciaridae, Diptera)

Abstract

ABSTRACT. Mariner-like elements are widely present in diverse organisms. These elements constitute a large fraction of the eukaryotic genome; they transpose by a "cut-and-paste" mechanism with their own transposase protein. We found two groups of mobile elements in the genus Rhynchosciara. PCR using primers designed from R. americana transposons (Ramar1 and Ramar2) were the starting point for this comparative study. Genomic DNA templates of four species: R. hollaenderi, R. millerii, R. baschanti, and Rhynchosciara sp were used and genomic sequences were amplified, sequenced and the molecular structures of the elements characterized as being putative mariner-like elements. The first group included the putative full-length elements. The second group was composed of defective mariner elements that contain a deletion overlapping most of the internal region of the transposase open reading frame. They were named Rmar1 (type 1) and Rmar2 (type 2), respectively. Many conserved amino acid blocks were identified, as well as a specific D,D(34)D signature motif that was defective in some elements. Based on predicted transposase sequences, these elements encode truncated proteins and are phylogenetically very close to mariner-like elements of the mauritiana subfamily. The inverted terminal repeat sequences that flanked the mariner-like elements are responsible for their mobility. These inverted terminal repeat sequences were identified by inverse PCR.

Molecular characterization of a mariner-like element in the Atta sexdens rubropilosa genome

“…To amplify mariner-like transposable elements in the A. s. rubropilosa genome the primers initially used were designed to amplify mariner elements of Rhynchosciara diptera (Rezende-Teixeira et al, 2010). Given the high identity observed between these elements, the primers functioned perfectly, and the ORF internal region of a mariner-like family element was amplified, as expected (pmar1R: 5ꞌ-TTTGCACAACAAGTTCAATTT-3ꞌ and pmar1F: 5ꞌ-TTTCTGGCAATTTACGGAT-3ꞌ).…”

“…Primers were designed for inverse PCR (iAsmar1R: 5ꞌ-TCCAATTAAAGCAGAAAATCAA-3ꞌ, iAsmar1F: 5ꞌ-TGGTGGGACTAAAAGGATCT-3ꞌ) based on the internal sequences of Asmar1. The protocol of DNA circularization was described in Rezende-Teixeira et al (2010). The PCR amplifications were performed using Platinum Taq DNA polymerase (Invitrogen Life Technologies) according to manufacturer instructions.…”