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

Ilya Kirov,Roman A Komakhin,Zakhar Konstantinov,Aleksey Ermolaev,Alexander Soloviev,Natalya Kudryavtseva,Sofya Gvaramiya,Maxim Dudnikov,Pavel Merkulov,Ekaterina Polkhovskaya,Gennady I Karlov,Mikhail G Divashuk,Marina Gilyok

doi:10.3390/plants10122681

Abstract

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.

Highlights

Transposable elements (TEs) are a major component of plant genomes, and up to 90% of the genome can be occupied by different transposable elements (TEs) families [1]
Several algorithms have been proposed for transposable element insertion (TEI) detection using short-read data, no ready-to-use solutions have been described for TE insertions (TEIs) detection using the low-coverage Oxford Nanopore Technology (ONT) reads
We present nanotei, a pipeline that allows the detection of TE insertions and TEcontained structural variants using a reference-guided approach

Summary

Introduction

Transposable elements (TEs) are a major component of plant genomes, and up to 90% of the genome can be occupied by different TE families [1]. The general impact of TEs on genome functionality is negative, they represent an important force of plant evolution, creating enormous genome variability [2]. The latest reports based on pangenome sequencing demonstrated that multiple traits involved in plant adaptation were tuned by TE insertions (TEIs) [3,4,5,6]. The inclusion of TEIs in association studies may bring new candidate loci associated with phenotypic variations, as demonstrated in tomato [9], rice [13] and other plants [11]. For example, TEIs were associated with variation in major agronomic traits [9,12]

Methods

Results

Conclusion