Bursts of retrotransposition reproduced in Arabidopsis

Tsukahara, Sayuri; Kobayashi, Akie; Kawabe, Akira; Mathieu, Olivier; Miura, Ai; Kakutani, Tetsuji

doi:10.1038/nature08351

Cited by 344 publications

(323 citation statements)

References 29 publications

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“…Rather, a combined outcome of many different family activities, some increased greatly, some less active, and some not amplifying at all, has been responsible for the great differences in Zea genome sizes. A similar story seems to hold true in Arabidopsis where, even under the influence of mutations that decrease the epigenetic silencing that keeps most TEs transcriptionally and transpositionally quiescent, activation of each of several families shows unique patterns of timing and amplification intensity (Tsukahara et al, 2009).…”

Section: Discussionmentioning

confidence: 93%

“…A more comprehensive analysis of TE behavior in a broader set of closely related lineages that differ in ploidy are needed to address this point. However, it is known that a large number of stress (Grandbastien, 1998) or genetic (Tsukahara et al, 2009) states can lead to a pulse of TE activation, which might take thousands or even millions of years to be fully suppressed by the plant host.…”

Section: Discussionmentioning

confidence: 99%

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The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

2013

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Sample sequence analysis was employed to investigate the repetitive DNAs that were most responsible for the evolved variation in genome content across seven panicoid grasses with 45-fold variation in genome size and different histories of polyploidy. In all cases, the most abundant repeats were LTR retrotransposons, but the particular families that had become dominant were found to be different in the Pennisetum, Saccharum, Sorghum and Zea lineages. One element family, Huck, has been very active in all of the studied species over the last few million years. This suggests the transmittal of an active or quiescent autonomous set of Huck elements to this lineage at the founding of the panicoids. Similarly, independent recent activity of Ji and Opie elements in Zea and of Leviathan elements in Sorghum and Saccharum species suggests that members of these families with exceptional activation potential were present in the genome(s) of the founders of these lineages. In a detailed analysis of the Zea lineage, the combined action of several families of LTR retrotransposons were observed to have approximately doubled the genome size of Zea luxurians relative to Zea mays and Zea diploperennis in just the last few million years. One of the LTR retrotransposon amplification bursts in Zea may have been initiated by polyploidy, but the great majority of transposable element activations are not. Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

2013

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“…Approximately 20% of the Arabidopsis genome (35) is comprised of TE-related sequences, which can vary in copy number and position among ecotypes (42)(43)(44). In addition, movement of TEs can cause CNV of nearby sequences (45)(46)(47).…”

Section: Resultsmentioning

confidence: 99%

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping

Chen

Copenhaver

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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DNA polymorphisms are important markers in genetic analyses and are increasingly detected by using genome resequencing. However, the presence of repetitive sequences and structural variants can lead to false positives in the identification of polymorphic alleles. Here, we describe an analysis strategy that minimizes false positives in allelic detection and present analyses of recently published resequencing data from Arabidopsis meiotic products and individual humans. Our analysis enables the accurate detection of sequencing errors, small insertions and deletions (indels), and structural variants, including large reciprocal indels and copy number variants, from comparisons between the resequenced and reference genomes. We offer an alternative interpretation of the sequencing data of meiotic products, including the number and type of recombination events, to illustrate the potential for mistakes in single-nucleotide polymorphism calling. Using these examples, we propose that the detection of DNA polymorphisms using resequencing data needs to account for nonallelic homologous sequences. Fig. 1 A and B). They can have phenotypic consequences and also serve as molecular markers for genetic analyses, facilitating linkage and association studies of genetic diseases, and other traits in humans (4-6), animals, plants, (7)(8)(9)(10) and other organisms. Using DNA polymorphisms for modern genetic applications requires low-error, high-throughput analytical strategies. Here, we illustrate the use of short-read nextgeneration sequencing (NGS) data to detect DNA polymorphisms in the context of whole-genome analysis of meiotic products.There are many methods for detecting SNPs (11-14) and structural variants (SVs) (15-25), including NGS, which can capture nearly all DNA polymorphisms (26-28). This approach has been widely used to analyze markers in crop species such as rice (29), genes associated with diseases (6, 26), and meiotic recombination in yeast and plants (30,31). However, accurate identification of DNA polymorphisms can be challenging, in part because short-read sequencing data have limited information for inferring chromosomal context.Genomes usually contain repetitive sequences that can differ in copy number between individuals (26-28, 31); therefore, resequencing analyses must account for chromosomal context to avoid mistaking highly similar paralogous sequences for polymorphisms. Here, we use recently published datasets to describe several DNA sequence features that can be mistaken as allelic (32, 33) and describe a strategy for differentiating between repetitive sequences and polymorphic alleles. We illustrate the effectiveness of these analyses by examining the reported polymorphisms from the published datasets.Meiotic recombination is initiated by DNA double-strand breaks (DSBs) catalyzed by the topoisomerase-like SPORULATION 11 (SPO11). DSBs are repaired as either crossovers (COs) between chromosomes (Fig. 1C), or noncrossovers (NCOs). Both COs and NCOs can be accompanied by gene conversion (GC) events, whic...

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“…27,28 In addition, the integrated DNA from a virus and/or transposon is inactivated by DNA methylation through a plant RNAi system. 29,30 What, then, is the function of DNAi in ferns? It is believed that ferns may have pathogenic resistance systems against fungi and viruses, although we could not find any report concerning the infection of a DNA virus in ferns.…”

Section: Discussionmentioning

confidence: 99%

Epigenetic memory of DNAi associated with cytosine methylation and histone modification in fern

Tsuboi

Sutoh

Wada

2012

Plant Signaling & Behavior

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Gene silencing technology, such as rNa interference (rNai), is commonly used to reduce gene expression in plant cells, and exogenous double-stranded rNa (dsrNa) can induce gene silencing in higher plants. Previously, we showed that the delivery of double-stranded DNa (dsDNa) fragments, such as Pcr products of an endogenous gene sequence, into fern (Adiantum capillus-veneris) gametophytic cells induces a sequence-specific gene silencing that we termed DNai. In this study, we used a neochrome 1 gene (NEO1) that mediates both red light-induced chloroplast movement and phototropism as a model of DNai and confirmed that the NEO1 function was suppressed by the repression of the NEO1 gene. Interestingly, the gene silencing effect by DNai was found in the progeny. cytosine methylation was detected in the NEO1-silenced lines. The DNa modifications was present in the transcriptional region of NEO1, but no differences between wild type and the silenced lines were found in the downstream region of NEO1. Our data suggest that the DNai gene silencing effect that was inherited throughout the next generation is regulated by epigenetic modification. Furthermore, the histone deacetylase inhibitor, trichostatin a (TSa), recovered the expression and function of NEO1 in the silenced lines, suggesting that histone deacetylation is essential for the direct suppression of target genes by DNai.

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Bursts of retrotransposition reproduced in Arabidopsis

Cited by 344 publications

References 29 publications

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping

Epigenetic memory of DNAi associated with cytosine methylation and histone modification in fern

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