The number of species with high-quality genome sequences continues to increase, in part due to the scaling up of multiple large-scale biodiversity sequencing projects. While the need to annotate genic sequences in these genomes is widely acknowledged, the parallel need to annotate transposable element (TE) sequences that have been shown to alter genome architecture, rewire gene regulatory networks, and contribute to the evolution of host traits is becoming ever more evident. However, accurate genome-wide annotation of TE sequences is still technically challenging. Several de novo TE identification tools are now available, but manual curation of the libraries produced by these tools is needed to generate high-quality genome annotations. Manual curation is time-consuming, and thus impractical for large-scale genomic studies, and lacks reproducibility. In this work, we present the Manual Curator Helper tool MCHelper, which automates the TE library curation process. By leveraging MCHelper's fully automated mode with the outputs from three de novo TE identification tools, RepeatModeler2, EDTA, and REPET, in the fruit fly, rice, hooded crow, zebrafish, maize, and human, we show a substantial improvement in the quality of the TE libraries and genome annotations. MCHelper libraries are less redundant, with up to 65% reduction in the number of consensus sequences, have up to 11.4% fewer false positive sequences, and up to ∼48% fewer “unclassified/unknown” TE consensus sequences. Genome-wide TE annotations are also improved, including larger unfragmented insertions. Moreover, MCHelper is an easy-to-install and easy-to-use tool.

中文翻译：

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MCHelper 自动管理真核生物物种的转座因子库


具有高质量基因组序列的物种数量持续增加，部分原因是多个大规模生物多样性测序项目的规模扩大。虽然注释这些基因组中的基因序列的需求已得到广泛认可，但同时需要注释转座因子 （TE） 序列，这些序列已被证明可以改变基因组结构、重新连接基因调控网络并有助于宿主性状的进化，这一点变得越来越明显。然而，TE 序列的准确全基因组注释在技术上仍然具有挑战性。现在有几种从头 TE 鉴定工具可用，但需要手动管理这些工具生成的文库才能生成高质量的基因组注释。手动管理非常耗时，因此对于大规模基因组研究不切实际，并且缺乏可重复性。在这项工作中，我们介绍了 Manual Curator Helper 工具 MCHelper，它可以自动化 TE 库管理过程。通过利用 MCHelper 的全自动模式以及果蝇、水稻、冠乌鸦、斑马鱼、玉米和人类的三种从头 TE 鉴定工具 RepeatModeler2、EDTA 和 REPET 的输出，我们展示了 TE 文库和基因组注释的质量有了显著提高。MCHelper 文库的冗余性较低，共有序列的数量减少了 65%，假阳性序列减少了 11.4%，“未分类/未知”的 TE 共有序列减少了 ∼48%。全基因组 TE 注释也得到了改进，包括更大的未片段化插入。此外，MCHelper 是一款易于安装且易于使用的工具。