DNA transposons are ubiquitous components of eukaryotic genomes. A major group of them encode a DDD/E transposase and contain terminal inverted repeats (TIRs) of varying lengths. The Kolobok superfamily of DNA transposons has been found in a wide spectrum of organisms. Here we report a new Kolobok lineage, designated KolobokP. They were identified in 7 animal phyla (Mollusca, Phoronida, Annelida, Nemertea, Bryozoa, Chordata, and Echinodermata), and are especially rich in bivalves. Unlike other Kolobok families, KolobokP adopts a composite-like architecture: an internal region (INT) flanked by two long terminal direct repeats (LTDRs), which exhibit their own short terminal inverted repeats ranging up to 18 bps. The excision of LTDRs was strongly suggested. The LTDR lengths seem to be constrained to be either around 450-bp or around 660-bp. The internal region encodes a DDD/E transposase and a small His-Me finger nuclease, which likely originated from the homing endonuclease encoded by a group I intron from a eukaryotic species. The architecture of KolobokP resembles composite DNA transposons, usually observed in bacterial genomes, and long terminal repeat (LTR) retrotransposons. In addition to this monomeric LTDR-INT-LTDR structure, plenty of solo LTDRs and multimers represented as (LTDR-INT)n-LTDR are also observed. Our structural and phylogenetic analysis supported the birth of KolobokP in the late stage of the Kolobok evolution. We propose KolobokP families propagate themselves in two ways: the canonical transposition catalyzed by their transposase and the sequence-specific cleavage by their endonuclease followed by the multimerization through the unequal crossover. The presence of homing endonuclease and long terminal direct repeats of KolobokP families suggest their unique dual replication mechanisms: transposition and induced unequal crossover.

中文翻译：

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编码 DDD/E 转座酶和 His-Me 手指归巢核酸内切酶的复合样 DNA 转座子的独特真核细胞谱系

DNA转座子是真核生物基因组中普遍存在的成分。它们中的一个主要组编码 DDD/E 转座酶并包含不同长度的末端反向重复 (TIR)。DNA 转座子的 Kolobok 超家族已在广泛的生物体中发现。在这里，我们报告了一个新的 Kolobok 谱系，指定为 KolobokP。它们在 7 个动物门（软体动物门、Phoronida、环节动物门、Nemertea、苔藓动物门、脊索动物门和棘皮动物门）中被发现，尤其富含双壳类动物。与其他 Kolobok 家族不同，KolobokP 采用类似复合的架构：内部区域 (INT) 两侧有两个长末端直接重复 (LTDR)，它们表现出自己的短末端反向重复，范围高达 18 bps。强烈建议切除 LTDR。LTDR 长度似乎被限制在 450 bp 左右或 660 bp 左右。内部区域编码一个 DDD/E 转座酶和一个小的 His-Me 指状核酸酶，这可能起源于真核物种的 I 组内含子编码的归巢核酸内切酶。KolobokP 的结构类似于通常在细菌基因组中观察到的复合 DNA 转座子和长末端重复 (LTR) 反转录转座子。除了这种单体 LTDR-INT-LTDR 结构外，还观察到大量单独的 LTDR 和表示为 (LTDR-INT)n-LTDR 的多聚体。我们的结构和系统发育分析支持 KolobokP 在 Kolobok 进化后期的诞生。我们建议 KolobokP 家族以两种方式自我繁殖：由它们的转座酶催化的规范转座和由它们的核酸内切酶催化的序列特异性切割，然后通过不等交叉进行多聚化。