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Article

Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline

1
All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
2
Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
3
Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia
*
Author to whom correspondence should be addressed.
Academic Editor: Khalid Meksem
Plants 2021, 10(12), 2681; https://doi.org/10.3390/plants10122681
Received: 3 November 2021 / Revised: 26 November 2021 / Accepted: 2 December 2021 / Published: 6 December 2021
Long-read data is a great tool to discover new active transposable elements (TEs). However, no ready-to-use tools were available to gather this information from low coverage ONT datasets. Here, we developed a novel pipeline, nanotei, that allows detection of TE-contained structural variants, including individual TE transpositions. We exploited this pipeline to identify TE insertion in the Arabidopsis thaliana genome. Using nanotei, we identified tens of TE copies, including ones for the well-characterized ONSEN retrotransposon family that were hidden in genome assembly gaps. The results demonstrate that some TEs are inaccessible for analysis with the current A. thaliana (TAIR10.1) genome assembly. We further explored the mobilome of the ddm1 mutant with elevated TE activity. Nanotei captured all TEs previously known to be active in ddm1 and also identified transposition of non-autonomous TEs. Of them, one non-autonomous TE derived from (AT5TE33540) belongs to TR-GAG retrotransposons with a single open reading frame (ORF) encoding the GAG protein. These results provide the first direct evidence that TR-GAGs and other non-autonomous LTR retrotransposons can transpose in the plant genome, albeit in the absence of most of the encoded proteins. In summary, nanotei is a useful tool to detect active TEs and their insertions in plant genomes using low-coverage data from Nanopore genome sequencing. View Full-Text
Keywords: transposon insertions; long read sequencing; structural variants; GAG; ddm1 transposon insertions; long read sequencing; structural variants; GAG; ddm1
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MDPI and ACS Style

Kirov, I.; Merkulov, P.; Dudnikov, M.; Polkhovskaya, E.; Komakhin, R.A.; Konstantinov, Z.; Gvaramiya, S.; Ermolaev, A.; Kudryavtseva, N.; Gilyok, M.; Divashuk, M.G.; Karlov, G.I.; Soloviev, A. Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline. Plants 2021, 10, 2681. https://doi.org/10.3390/plants10122681

AMA Style

Kirov I, Merkulov P, Dudnikov M, Polkhovskaya E, Komakhin RA, Konstantinov Z, Gvaramiya S, Ermolaev A, Kudryavtseva N, Gilyok M, Divashuk MG, Karlov GI, Soloviev A. Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline. Plants. 2021; 10(12):2681. https://doi.org/10.3390/plants10122681

Chicago/Turabian Style

Kirov, Ilya, Pavel Merkulov, Maxim Dudnikov, Ekaterina Polkhovskaya, Roman A. Komakhin, Zakhar Konstantinov, Sofya Gvaramiya, Aleksey Ermolaev, Natalya Kudryavtseva, Marina Gilyok, Mikhail G. Divashuk, Gennady I. Karlov, and Alexander Soloviev. 2021. "Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline" Plants 10, no. 12: 2681. https://doi.org/10.3390/plants10122681

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