Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia.
Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia.
Methods Mol Biol. 2023;2703:31-44. doi: 10.1007/978-1-0716-3389-2_3.
LTR retrotransposons (LTR-RT) are major components of plant genomes. These transposable elements participate in the structure and evolution of genes and genomes through their mobility and their copy number amplification. For example, they are commonly used as evolutionary markers in genetic, genomic, and cytogenetic approaches. However, the plant research community is faced with the near absence of free availability of full-length, curated, and lineage-level classified LTR retrotransposon reference sequences. In this chapter, we will introduce InpactorDB, an LTR retrotransposon sequence database of 181 plant species representing 98 plant families for a total of 67,241 non-redundant elements. We will introduce how to use newly sequenced genomes to identify and classify LTR-RTs in a similar way with a standardized procedure using the Inpactor tool. InpactorDB is freely available at https://inpactordb.github.io .
长末端重复转座子 (LTR-RT) 是植物基因组的主要组成部分。这些可移动元件通过其移动性和拷贝数扩增参与基因和基因组的结构和进化。例如，它们通常被用作遗传、基因组和细胞遗传学方法中的进化标记。然而，植物研究界面临着缺乏完整的、经过精心整理的、基于谱系分类的 LTR 逆转录转座子参考序列的问题。在本章中，我们将介绍 InpactorDB，这是一个包含 181 种植物物种的 LTR 逆转录转座子序列数据库，代表 98 个植物科，共有 67241 个非冗余元件。我们将介绍如何使用新测序的基因组，以类似于使用 Inpactor 工具的标准化程序来识别和分类 LTR-RTs。InpactorDB 可在 https://inpactordb.github.io 免费获取。
