Transpositional landscape of the rice genome revealed by paired‐end mapping of high‐throughput re‐sequencing data

Abstract

). † These authors contributed equally to this work. SUMMARYTransposable elements (TEs) are mobile entities that densely populate most eukaryotic genomes and contribute to both their structural and functional dynamics. However, most TE-related sequences in both plant and animal genomes correspond to inactive, degenerated elements, due to the combined effect of silencing pathways and elimination through deletions. One of the major difficulties in fully characterizing the molecular basis of genetic diversity of a given species lies in establishing its genome-wide transpositional activity. Here, we provide an extensive survey of the transpositional landscape of a plant genome using a deep sequencing strategy. This was achieved through paired-end mapping of a fourfold coverage of the genome of rice mutant line derived from an in vitro callus culture using Illumina technology. Our study shows that at least 13 TE families are active in this genotype, causing 34 new insertions. This next-generation sequencing-based strategy provides new opportunities to quantify the impact of TEs on the genome dynamics of the species.

Use of Next Generation Sequencing (NGS) Technologies for the Genome-Wide Detection of Transposition

“…In this regard, high quality refers to the fi nal assembly of the pseudomolecules of the completed genomic sequence. So far in plants, PairedEnd Mapping (PEM) for the detection of transposition was successfully applied on the two species for which a high quality assembly based on a physical map is available, i.e., rice [ 9 ] and Arabidopsis thaliana [ 6 ].…”

“…This pipeline was recently used to identify active TEs in rice [ 9 ]. Our strategy is based on the detection of homology breakpoints between paired end reads in a given genome when compared to a reference genome.…”

Mechanisms of Transposable Element Evolution in Plants and Their Effects on Gene Expression

“…Deletions can occur through two types of ectopic recombination: illegitimate recombination (IR), which utilizes only short regions of homology and does not require RecA, and unequal homologous recombination (UHR) between direct repeats with high homology [90,118,119,[127][128][129]. In the case of LTR retrotransposons, the deletion of one LTR and the rest of the TE sequences between the LTRs of a retrotransposon via UHR leaves a single LTR called a solo-LTR (Fig.…”

“…For example, higher TE transposition and/or transcription rates have been noted after heat shock (e.g., [95,158]), cold stress (e.g., [159][160][161]), pathogen/microbe infection (e.g., [162,163]), high-ultraviolet (UV) exposure (e.g., [164]), and wounding (e.g., [36,159]). [107], while in rice at least 13 TE families are transpositionally activated in in vitro culture [129]. In some cases, such as the tobacco Tto1 class I TE under pathogen stress, activation of the TE may result from convergent evolution within the TE promoter resulting in transcription factor-binding sites that are utilized under particular conditions [18,163].…”

Genome-wide profiling of genetic variation in Agrobacterium-transformed rice plants

“…S4). Because the in vitro culture process is known to cause somaclonal variation (Sabot et al, 2011), we analyzed one transgenic T 0 line (T204) having an extended in vitro culture period (about 5 months) and four T 0 lines (T027, T182, T273, and T400) with a short culture period (about 3 months) (Fig. S5).…”