engleski

MITE - like elements with internal tandem repeats in the Pacific oyster Crassostrea gigas (Thunberg, 1796)

The Pacific oyster Crassostrea gigas (Thunberg, 1793) is a marine bivalve (class Bivalvia) known as commercially the most important oyster species in the world. Recently sequenced genome of this species showed abundance of repetitive sequences that comprise ~36% of the genome and include some transposable elements (TEs) still being active. MITE (miniature inverted-repeat transposable element) elements were estimated to constitute 8, 8% of the genome. Recent research performed in our laboratory shows that the clam Donax trunculus genome is populated by MITE-related interspersed repetitive DNA sequences that bear short arrays of tandem repeats, connecting in this way satellite DNAs and TEs (Genome Biol. Evol. 5:2549). The described MITE elements are characterized by a modular structure composed of the left conserved region, followed by a spacer sequence of different length (app. 70-160 bp), internal tandem repeats (1-6), an imperfect microsatellite repeat motif (ACRG)n and a conserved right region. Imperfect inverted repeats (app. 10-20 bp) are located at terminal and subterminal positions and elements are flanked with two-nucleotide target site duplications. Here we report three new elements which correspond to the described modular structure. Elements named Cragi 1, Cragi 2 and Cragi 3 are found by bioinformatic analysis of the assembled genome of the oyster C. gigas. Although Cragi elements share a similar microsatellite motif, their sequences are different in all other modules – the left and right flanking sequences, and the internal tandem repeats. The number of internal tandem repeats is variable within an element, and in Cragi elements can be up to 12, what is twice more than in previously described MITE–like elements. While Cragi 1 internal tandem repeats show 80% sequence similarity with the highly abundant Cg170 satellite DNA already described in C. gigas, internal repeats of the other two elements do not reveal similarity with any known satellite DNA. Further research is in progress to resolve if Cragi 2 and Cragi 3 repeats can be present as autonomous units repeated in tandem and form arrays typical for satellite DNAs. It was also noted that all three whole-length Cragi elements show a high degree of sequence similarity with eukaryotic rolling-circle transposons known as Helitrons. Here we propose that Helitron-related TEs bearing internal tandem repeats might be an initial form from which satellite DNA spread begins.

MITE; transposable elements; satellite DNA

nije evidentirano