Table_2_MegaLTR: a web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes.xlsx

LTR-retrotransposons (LTR-RTs) are a class of RNA-replicating transposon elements (TEs) that can alter genome structure and function by moving positions, repositioning genes, shifting exons, and causing chromosomal rearrangements. LTR-RTs are widespread in many plant genomes and constitute a significant portion of the genome. Their movement and activity in eukaryotic genomes can provide insight into genome evolution and gene function, especially when LTR-RTs are located near or within genes. Building the redundant and non-redundant LTR-RTs libraries and their annotations for species lacking this resource requires extensive bioinformatics pipelines and expensive computing power to analyze large amounts of genomic data. This increases the need for online services that provide computational resources with minimal overhead and maximum efficiency. Here, we present MegaLTR as a web server and standalone pipeline that detects intact LTR-RTs at the whole-genome level and integrates multiple tools for structure-based, homologybased, and de novo identification, classification, annotation, insertion time determination, and LTR-RT gene chimera analysis. MegaLTR also provides statistical analysis and visualization with multiple tools and can be used to accelerate plant species discovery and assist breeding programs in their efforts to improve genomic resources. We hope that the development of online services such as MegaLTR, which can analyze large amounts of genomic data, will become increasingly important for the automated detection and annotation of LTR-RT elements.

LTR-逆转录转座子（LTR-RTs）是一类RNA复制转座子元件（TEs），它们可以通过移动位置、重新定位基因、移位外显子以及引起染色体重排来改变基因组结构和功能。LTR-RTs在许多植物基因组中广泛存在，并构成了基因组的重要组成部分。它们在真核基因组中的移动和活动可以为基因组进化和基因功能提供洞见，尤其是在LTR-RTs位于或处于基因附近或内部时。构建缺乏此类资源的物种的冗余和非冗余LTR-RTs库及其注释需要庞大的生物信息学管道和昂贵的计算能力来分析大量的基因组数据。这增加了对提供最小化开销和最大化效率的计算资源的在线服务的需求。在此，我们介绍了MegaLTR作为一款网络服务器和独立流程，该流程能够在全基因组水平上检测完整的LTR-RTs，并集成多种基于结构、基于同源和从头开始的识别、分类、注释、插入时间确定以及LTR-RTs基因嵌合体分析的工具。MegaLTR还提供了多种工具的统计分析与可视化，可用于加速植物物种的发现，并协助育种计划在改善基因组资源方面的努力。我们期望，像MegaLTR这样的在线服务，能够分析大量基因组数据的发展，将为LTR-RTs元素的自动化检测和注释变得日益重要。