Background The Tc1/mariner superfamily might represent the most diverse and widely distributed group of DNA transposons. Several families have been identified; however, exploring the diversity of this superfamily and updating its classification is still ongoing in the life sciences. Results Here we identified a new family of Tc1/mariner transposons, named Incomer (IC), which is close to, but distinct from the known family DD34E/Tc1. ICs have a total length of about 1.2 kb, and harbor a single open reading frame encoding a ~ 346 amino acid transposase with a DD36E motif and flanked by short terminal inverted repeats (TIRs) (22-32 base pairs, bp). This family is absent from prokaryotes, and is mainly distributed among vertebrates (141 species of four classes), including Agnatha (one species of jawless fish), Actinopterygii (132 species of ray-finned fish), Amphibia (four species of frogs), and Mammalia (four species of bats), but have a restricted distribution in invertebrates (four species in Insecta and nine in Arachnida). All ICs in bats (Myotis lucifugus, Eptesicus fuscus, Myotis davidii, and Myotis brandtii) are present as truncated copies in these genomes, and most of them are flanked by relatively long TIRs (51-126 bp). High copy numbers of miniature inverted-repeat transposable elements (MITEs) derived from ICs were also identified in bat genomes. Phylogenetic analysis revealed that ICs are more closely related to DD34E/Tc1 than to other families of Tc1/mariner (e.g., DD34D/mariner and DD × D/pogo), and can be classified into four distinct clusters. The host and IC phylogenies and pairwise distance comparisons between RAG1 genes and all consensus sequences of ICs support the idea that multiple episodes of horizontal transfer (HT) of ICs have occurred in vertebrates. In addition, the discovery of intact transposases, perfect TIRs and target site duplications of ICs suggests that this family may still be active in Insecta, Arachnida, frogs, and fish. Conclusions Exploring the diversity of Tc1/mariner transposons and revealing their evolutionary profiles will help provide a better understanding of the evolution of DNA transposons and their impact on genomic evolution. Here, a newly discovered family (DD36E/Incomer) of Tc1/mariner transposons is described in animals. It displays a similar structural organization and close relationship with the known DD34E/Tc1 elements, but has a relatively narrow distribution, indicating that DD36E/IC might have originated from the DD34E/Tc1 family. Our data also support the hypothesis of horizontal transfer of IC in vertebrates, even invading one lineage of mammals (bats). This study expands our understanding of the diversity of Tc1/mariner transposons and updates the classification of this superfamily.

中文翻译：

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Incomer，一个在动物中新发现的 DD36E Tc1/mariner 转座子家族。

背景 Tc1/mariner 超家族可能代表最多样化和分布最广的 DNA 转座子组。已经确定了几个家庭；然而，探索这个超家族的多样性并更新其分类仍在生命科学领域进行。结果 在这里，我们确定了一个新的 Tc1/mariner 转座子家族，命名为 Inmerr (IC)，它与已知的家族 DD34E/Tc1 很接近，但又不同。IC 的总长度约为 1.2 kb，具有一个单一的开放阅读框，该框架编码一个具有 DD36E 基序的约 346 个氨基酸转座酶，其两侧是短末端反向重复序列 (TIR)（22-32 个碱基对，bp）。该科在原核生物中不存在，主要分布在脊椎动物（四纲 141 种）中，包括 Agnatha（一种无颌鱼），Actinopterygii（132 种鳍鱼）、两栖动物（四种青蛙）和哺乳动物（四种蝙蝠），但在无脊椎动物中分布有限（昆虫纲 4 种，蛛形纲动物 9 种）。蝙蝠中的所有 IC（Myotis lucifugus、Eptesicus fuscus、Myotis davidii 和 Myotis brandtii）在这些基因组中都以截短拷贝的形式存在，并且它们中的大多数两侧都有相对较长的 TIR（51-126 bp）。在蝙蝠基因组中也发现了源自 IC 的高拷贝数的微型反向重复转座因子 (MITE)。系统发育分析表明，ICs 与 DD34E/Tc1 的关系比与 Tc1/mariner 的其他家族（例如，DD34D/mariner 和 DD × D/pogo）更密切相关，并且可以分为四个不同的簇。宿主和 IC 系统发育以及 RAG1 基因与 IC 的所有共有序列之间的成对距离比较支持了在脊椎动物中发生了 IC 的多次水平转移 (HT) 事件的观点。此外，完整转座酶、完美 TIR 和 IC 靶位点重复的发现表明该家族可能在昆虫纲、蛛形纲、青蛙和鱼类中仍然活跃。结论 探索 Tc1/mariner 转座子的多样性并揭示它们的进化谱将有助于更好地理解 DNA 转座子的进化及其对基因组进化的影响。在这里，在动物中描述了一个新发现的 Tc1/mariner 转座子家族 (DD36E/Incomer)。它显示出与已知的 DD34E/Tc1 元素相似的结构组织和密切关系，但分布相对狭窄，表明 DD36E/IC 可能起源于 DD34E/Tc1 家族。我们的数据还支持 IC 在脊椎动物中水平转移的假设，甚至入侵了哺乳动物（蝙蝠）的一个谱系。这项研究扩展了我们对 Tc1/mariner 转座子多样性的理解，并更新了这个超家族的分类。