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 similarity 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 considerably 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 duplication, and the potential of the 3' end to participate in formation of non-autonomous derivatives.

中文翻译：

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真核生物类佩内洛普元素的分布和系统发育

Penelope 样元件 (PLEs) 是一类研究相对较少的真核逆转录元件，其特点是存在 GIY-YIG 核酸内切酶结构域、一些代表保留内含子的能力以及 PLE 编码的逆转录酶与端粒酶的相似性。尽管这些逆转录转座子在许多动物基因组中很丰富，但逆转录酶部分也可以在几种原生生物、真菌和植物中找到，这表明它的古老起源。基于扩展的序列比对和显着扩展的数据集，对 PLE 进行了全面的系统发育分析。PLE 表现出类似于非 LTR 逆转录转座子的进化模式，它们形成可追溯到前寒武纪时代的深分支进化枝。然而，PLE 似乎比非 LTR 逆转录转座子经历了更高程度的谱系损失。建议将 PLEs 和非 LTR 逆转录转座子纳入更大的 eTPRT（真核靶标引发）逆转录元件组，其特征是 5' 截断、可变靶位点重复和 3' 末端参与形成的潜力非自治衍生品。