Mokhtar Morad M, El Allali Achraf
African Genome Center, Mohammed VI Polytechnic University, Benguerir, Morocco.
Front Plant Sci. 2023 Sep 20;14:1237426. doi: 10.3389/fpls.2023.1237426. eCollection 2023.
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 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.
长末端重复序列逆转座子（LTR-RTs）是一类RNA复制转座子元件（TEs），可通过移动位置、重新定位基因、转移外显子和引起染色体重排来改变基因组结构和功能。LTR-RTs广泛存在于许多植物基因组中，占基因组的很大一部分。它们在真核生物基因组中的移动和活性有助于深入了解基因组进化和基因功能，特别是当LTR-RTs位于基因附近或基因内部时。对于缺乏此类资源的物种，构建冗余和非冗余LTR-RTs文库及其注释需要广泛的生物信息学流程和昂贵的计算能力来分析大量基因组数据。这增加了对在线服务的需求，这些服务能够以最小的开销和最高的效率提供计算资源。在此，我们展示了MegaLTR，它作为一个网络服务器和独立流程，可在全基因组水平上检测完整的LTR-RTs，并集成了多种工具用于基于结构、基于同源性的鉴定、分类、注释、插入时间确定以及LTR-RT基因嵌合体分析。MegaLTR还通过多种工具提供统计分析和可视化，可用于加速植物物种发现，并协助育种计划改进基因组资源。我们希望像MegaLTR这样能够分析大量基因组数据的在线服务的开发，对于LTR-RT元件的自动检测和注释将变得越来越重要。
