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. 2023:2703:31-44.
doi: 10.1007/978-1-0716-3389-2_3.

InpactorDB: A Plant LTR Retrotransposon Reference Library

Simon Orozco-Arias  1   2 , Simon Gaviria-Orrego  1 , Reinel Tabares-Soto  3   2 , Gustavo Isaza  2 , Romain Guyot  4   5
Affiliations

InpactorDB: A Plant LTR Retrotransposon Reference Library

Simon Orozco-Arias et al. Methods Mol Biol. 2023.

Abstract

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 .

Keywords: Database; LTR retrotransposons; LTR-RT identification and annotation; Lineage level; Plants.

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References

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