New LTR Retrotransposable Elements from Eukaryotic Genomes

Abstract

LTR retrotransposons have been identified in the genomes of many eukaryotic organisms. Several approaches can be used in order to identify new LTR retrotransposons from a wide range of organisms. One of them is a systematic search of genomic sequences generated from whole genome sequencing projects. Here, we performed a computer analysis of 14 genomes with the aim of extracting LTR retrotransposons using a software based on the hidden Markov models. Altogether, 24 new LTR retrotransposable elements from 4 subclasses Ty3/gypsy, DIRS, Bel, and Ty1/copia were identified in 9 different genomes. A new family of retroelements was obtained after the analysis of the genomes of ascomycetes and basidiomycetes fungi. Considerable differences in the amount and diversity of retroelements were detected in the distantly related nematodes B. malayi and C. briggsae. Finally, our analysis did not reveal the presence of LTR retroelements in the genomes of parasitic protozoan.