LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

Disdero, Eric; Filée, Jonathan

doi:10.1186/s13100-017-0088-x

Cited by 29 publications

(20 citation statements)

References 23 publications

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“…Their repetitive nature and large size (e.g., the Ty1 is approximately 6 kb) present major challenges to genome assembly, and traditional alignment pipelines will miss new insertions due to their absence in the reference genome. There have been many advances in the computational detection of TEs using short read sequencing data ( Ewing 2015 ; Rishishwar et al 2017 ), and long-read sequencing will likely represent the new gold standard for TE annotation ( Disdero and Filée 2017 ; Bergman 2018 ; Kutter et al 2018 ; Shahid and Slotkin 2020 ). However, there is still a wide range of false positives and false negatives associated with computational methods, and long-read sequencing is currently more expensive and less high-throughput than short read methods.…”

Section: Resultsmentioning

confidence: 99%

Transposable Element Mobilization in Interspecific Yeast Hybrids

Heil

Patterson

Hickey

et al. 2021

Genome Biology and Evolution

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Barbara McClintock first hypothesized that interspecific hybridization could provide a “genomic shock” that leads to the mobilization of transposable elements. This hypothesis is based on the idea that regulation of transposable element movement is potentially disrupted in hybrids. However, the handful of studies testing this hypothesis have yielded mixed results. Here, we set out to identify if hybridization can increase transposition rate and facilitate colonization of transposable elements in Saccharomyces cerevisiae x Saccharomyces uvarum interspecific yeast hybrids. S. cerevisiae have a small number of active long terminal repeat (LTR) retrotransposons (Ty elements), while their distant relative S. uvarum have lost the Ty elements active in S. cerevisiae. While the regulation system of Ty elements is known in S. cerevisiae, it is unclear how Ty elements are regulated in other Saccharomyces species, and what mechanisms contributed to the loss of most classes of Ty elements in S. uvarum. Therefore, we first assessed whether transposable elements could insert in the S. uvarum sub-genome of a S. cerevisiae x S. uvarum hybrid. We induced transposition to occur in these hybrids and developed a sequencing technique to show that Ty elements insert readily and non-randomly in the S. uvarum genome. We then used an in vivo reporter construct to directly measure transposition rate in hybrids, demonstrating that hybridization itself does not alter rate of mobilization. However, we surprisingly show that species-specific mitochondrial inheritance can change transposition rate by an order of magnitude. Overall, our results provide evidence that hybridization can potentially facilitate the introduction of transposable elements across species boundaries and alter transposition via mitochondrial transmission, but that this does not lead to unrestrained proliferation of transposable elements suggested by the genomic shock theory.

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Section: Resultsmentioning

confidence: 99%

Transposable Element Mobilization in Interspecific Yeast Hybrids

Heil

Patterson

Hickey

et al. 2021

Genome Biology and Evolution

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“…For example, the short length of the next-generation sequencing reads causes drastic ambiguity and imprecision in mapping the TE reads. Recent advance of the long read sequencing of PacBio ( Disdero and Filée, 2017 ) and Oxford Nanopore ( Debladis et al, 2017 ) is expected to overcome this shortcoming. In addition, due to the multiplicity of TEs in the genome and possible redundancy between them, the genetic analyses of TEs have been challenging.…”

Section: Discussionmentioning

confidence: 99%

Transposon-Derived Non-coding RNAs and Their Function in Plants

Cho

2018

Front. Plant Sci.

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Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans-acting regulatory roles of TE-derived RNAs have been rarely studied. It was only recently that TEs were investigated for their regulatory roles as a form of RNA. Particularly in plants, TEs are ample source of small RNAs such as small interfering (si) RNAs and micro (mi) RNAs. Those TE-derived small RNAs have potentials to affect non-TE transcripts by sequence complementarity, thereby generating novel gene regulatory networks including stress resistance and hybridization barrier. Apart from the small RNAs, a number of long non-coding RNAs (lncRNAs) are originated from TEs in plants. For example, a retrotransposon-derived lncRNA expressed in rice root acts as a decoy RNA or miRNA target mimic which negatively controls miRNA171. The post-transcriptional suppression of miRNA171 in roots ensures the stabilization of the target transcripts encoding SCARECROW-LIKE transcription factors, the key regulators of root development. In this review article, the recent discoveries of the regulatory roles of TE-derived RNAs in plants will be highlighted.

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“…Others on the contrary map first to the consensus sequence of previously identified TEs and map afterwards the paired read onto the genome, such as TRACKPOSON [108]. A more recent approach using long Pacbio reads has also been reported, but it still relies on the good annotation of reference TE sequences [109]. Another approach infers insertion events using the misalignment and split alignment of short reads without relying on a database of previously identified TEs.…”

Section: Bioinformatic Analysis Of Te Sequences In Genomesmentioning

confidence: 99%

On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

Lerat

Casacuberta

Chaparro

et al. 2019

Genes

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Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. Although some TE insertions could provide adaptive advantages to species, transposition is a highly mutagenic event that has to be tightly controlled to ensure its viability. Genomes have evolved sophisticated mechanisms to control TE activity, the most important being epigenetic silencing. However, the epigenetic control of TEs can also affect genes located nearby that can become epigenetically regulated. It has been proposed that the combination of TE mobilization and the induced changes in the epigenetic landscape could allow a rapid phenotypic adaptation to global environmental changes. In this review, we argue the crucial need to take into account the repeated part of genomes when studying the global impact of epigenetic modifications on an organism. We emphasize more particularly why it is important to carefully consider TEs and what bioinformatic tools can be used to do so.

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LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

Cited by 29 publications

References 23 publications

Transposable Element Mobilization in Interspecific Yeast Hybrids

Transposable Element Mobilization in Interspecific Yeast Hybrids

Transposon-Derived Non-coding RNAs and Their Function in Plants

On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

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