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.
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Acknowledgments
The authors acknowledge the IFB Core Cluster that is part of the National Network of Compute Resources (NNCR) of the Institut Français de Bioinformatique (https://www.france-bioinformatique.fr) and the IRD itrop (https://bioinfo.ird.fr/) at IRD Montpellier for providing HPC resources that have contributed to the research results reported in this paper. The authors thank the LMI BIO_INCA (bioinca.org), the STICAMSUD 21-STIC-13, ECOS-Nord C21MA01, and Minciencias Grant Call 785/2017 for providing support. The authors declare there is no competing financial interest.
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Orozco-Arias, S., Gaviria-Orrego, S., Tabares-Soto, R., Isaza, G., Guyot, R. (2023). InpactorDB: A Plant LTR Retrotransposon Reference Library. In: Garcia, S., Nualart, N. (eds) Plant Genomic and Cytogenetic Databases. Methods in Molecular Biology, vol 2703. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3389-2_3
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DOI: https://doi.org/10.1007/978-1-0716-3389-2_3
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