Distribution and phylogeny of penelope-like elements in eukaryotes

Abstract.—Penelope-like elements (PLEs) are a relatively little studied class of eukaryotic retroelements, distinguished by the presence of the GIY-YIG endonuclease domain, the ability of some representatives to retain introns, and the similar-ity of PLE-encoded reverse transcriptases to telomerases. Although these retrotransposons are abundant in many animal genomes, the reverse transcriptase moiety can also be found in several protists, fungi, and plants, indicating its ancient origin. A comprehensive phylogenetic analysis of PLEs was conducted, based on extended sequence alignments and a con-siderably expanded data set. PLEs exhibit the pattern of evolution similar to that of non-LTR retrotransposons, which form deep-branching clades dating back to the Precambrian era. However, PLEs seem to have experienced a much higher degree of lineage losses than non-LTR retrotransposons. It is suggested that PLEs and non-LTR retrotransposons are included into a larger eTPRT (eukaryotic target-primed) group of retroelements, characterized by 5 ' truncation, variable target-site dupli-cation, and the potential of the 3 ' end to participate in formation of non-autonomous derivatives. [Penelope-like elements; retrotransposons; reverse transcriptase; GIY-YIG endonuclease.] One of the biggest surprises that the whole-genome sequencing era has brought to us is the amount of non-genic, and especially transposable element-derived, se-quences that comprise the bulk of chromosomal DN