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Genomic re-assessment of the transposable element landscape of the potato genome

Abstract

Key message

We provide a comprehensive and reliable potato TE landscape, based on a wide variety of identification tools and integrative approaches, producing clear and ready-to-use outputs for the scientific community.

Abstract

Transposable elements (TEs) are DNA sequences with the ability to autoreplicate and move throughout the host genome. TEs are major drivers in stress response and genome evolution. Given their significance, the development of clear and efficient TE annotation pipelines has become essential for many species. The latest de novo TE discovery tools, along with available TEs from Repbase and sRNA-seq data, allowed us to perform a reliable potato TEs detection, classification and annotation through an open-source and freely available pipeline (https://github.com/DiegoZavallo/TE_Discovery). Using a variety of tools, approaches and rules, we were able to provide a clearly annotated of characterized TEs landscape. Additionally, we described the distribution of the different types of TEs across the genome, where LTRs and MITEs present a clear clustering pattern in pericentromeric and subtelomeric/telomeric regions respectively. Finally, we analyzed the insertion age and distribution of LTR retrotransposon families which display a distinct pattern between the two major superfamilies. While older Gypsy elements concentrated around heterochromatic regions, younger Copia elements located predominantly on euchromatic regions. Overall, we delivered not only a reliable, ready-to-use potato TE annotation files, but also all the necessary steps to perform de novo detection for other species.

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Acknowledgements

The authors would like to thank Dr. Soledad Lucero and Dr. Julia Sabio y Garcia for the assistance with English-language editing, Humberto Julio Debat for his critical comments on the manuscript and Eng. Juan Cecconi for his informatics assistance and critical discussion. This work was supported by the Instituto Nacional de Tecnología Agropecuaria (INTA) and by ANPCyT PICT 2015-1532 and PICT 2016-0429. The funders had no role in this study design, data collection and analysis, decision to publish or preparation of the manuscript.

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Correspondence to Diego Zavallo or Sebastian Asurmendi.

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Communicated by Neal Stewart.

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Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Fasta files containing family sequences for each type transposon elements (FASTA 10814 kb)

Supplementary material 2 (FASTA 11 kb)

Supplementary material 3 (FASTA 298 kb)

Supplementary material 4 (FASTA 68282 kb)

Supplementary material 5 (FASTA 1602 kb)

Supplementary material 6 (FASTA 8 kb)

Supplementary material 7 (FASTA 5510 kb)

Supplementary material 8 (FASTA 2118 kb)

Word document containing comparative analysis between RepeatMasker library and our pipeline TEs libraries (PDF 1438 kb)

gff3 file containing all TEs copy coordinates from our pipeline, including Chr00 (GFF3 35827 kb)

gff3 file containing not overlapped elements coordinates from Repeat Masker library, including Chr00 (GFF3 19266 kb)

Table summarizing metrics of TEs to the nearest genes (XLSX 9 kb)

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Zavallo, D., Crescente, J.M., Gantuz, M. et al. Genomic re-assessment of the transposable element landscape of the potato genome. Plant Cell Rep 39, 1161–1174 (2020). https://doi.org/10.1007/s00299-020-02554-8

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  • DOI: https://doi.org/10.1007/s00299-020-02554-8

Keywords

  • Transposable elements
  • Solanum tuberosum
  • Potato
  • TEs annotation
  • Retrotransposons
  • DNA transposons