Exaptation of transposable element coding sequences

Joly‐Lopez, Zoé; Bureau, Thomas E.

doi:10.1016/j.gde.2018.02.011

Cited by 60 publications

(48 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We found that these TEs have substantially lower CG methylation in the VC than in sperm at and near the TSS ( Figure 1D,E , Figure 1—figure supplement 1D ), indicative of DME activity. Because TEs tend to be flanked by repeats (Joly-Lopez & Bureau, 2018), the transcriptional termination site (TTS) regions of activated TEs also tend to be hypomethylated in the VC ( Figure 1D,E , Figure 1— figure supplement 1D ). Examination of DNA methylation in VCs from dme/+ heterozygous plants ( dme homozygous mutants are embryonic lethal), which produce a 50:50 ratio of dme mutant and WT pollen, revealed partial restoration of methylation at TSS and TTS of VC-activated TEs ( Figure 1D,E) .…”

Section: Resultsmentioning

confidence: 99%

Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation

Vickers

Zhang

et al. 2018

Preprint

View full text Add to dashboard Cite

10Transposable elements (TEs), the movement of which can damage the genome, are 11 epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion 12 cell -vegetative cell (VC) -of the flowering plant Arabidopsis thaliana. However, the extent 13 and mechanism of this activation are unknown. Here we show that about 100 heterochromatic 14 TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further 15 demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion 16 of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing 17 DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 18 is required for heterochromatin condensation in plant cells and show that H1 overexpression 19 creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate 20 that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed 21 DNA demethylation, heterochromatin relaxation, and TE activation.22 23 84

show abstract

Section: Resultsmentioning

confidence: 99%

Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation

Vickers

Zhang

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…A genome which has retained the original characteristics of the ancestral magnoliid lineage, will be an invaluable resource for future studies on angiosperm early diversification. The apparent stability of the Annona genome over time is notable given that gene family expansion (such as in (Chaw et al 2019 increase of transposable elements (Belyayev 2014;Joly-Lopez and Bureau 2018) and WGD events (Hoffman et al 2012) are potential triggers of morphological or adaptive key innovations and rapid diversification (Tank et al 2015;Soltis and Soltis 2016). These aspects raise further questions regarding the origin and evolutionary mechanisms giving rise to the diversity of magnoliids (Sauquet and Magallón 2018).…”

Section: Discussionmentioning

confidence: 99%

The soursop genome and comparative genomics of basal angiosperms provide new insights on evolutionary incongruence

Strijk¹,

Hinsinger²,

Mm³

et al. 2019

Preprint

View full text Add to dashboard Cite

Deep relationships and the sequence of divergence among major lineages of angiosperms (magnoliids, monocots and eudicots) remain ambiguous and differ depending on analytical approaches and datasets used.Complete genomes potentially provide opportunities to resolve these uncertainties, but two recently published magnoliid genomes instead deliver further conflicting signals. To disentangle key angiosperm relationships, we report a high-quality draft genome for the soursop (Annona muricata, Annonaceae). We reconstructed phylogenomic trees and show that the soursop represents a genomic mosaic supporting different histories, with scaffolds almost exclusively supporting single topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previous whole genome-based studies remained inconclusive. This result is clear and consistent with recent studies using plastomes. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history. 36 37 38 39 40 41 42 43 44 45 46 47 2 successive reductions in the number of whorls of both the perianth and the androecium. In both cases, disparate reductions may have paved the way for the evolution of clade specific features of genomes and flower morphology in contemporary clades. Since the publication of the first plant genome, that of Arabidopsis thaliana (Initiative 2000), there has been a steady increase in the number of sequenced eudicot and monocot genomes. However, with the exception of the iconic Amborella trichopoda, basal angiosperm diversity represented by the ancient lineages of Nymphaeales, Austrobaileyales, Chloranthales, and magnoliids has largely been overlooked. After eudicots and monocots, Magnoliidae are the most diverse clade of angiosperms (Massoni et al. 2014) with 9,000-10,000 species in four orders (Canellales, Piperales, Laurales and Magnoliales). However, despite this diversity and economic value (e.g. avocado, black pepper, cinnamon, soursop), only two genomes have been

show abstract

“…The observed level of polymorphism for AALF020122 with AlbRha52, AALF025780 with AlbRha12, and AALF005432 with AlbFlavi34 is analogous to that of rapidly evolving genes, suggesting co-option for immunity functions (Frank and Feschotte 2017). Because domestication of exogenous sequences is a multi-step process, including persistence, immobilization and stable expression of the newly-acquired sequences besides rapid evolution (Joly-Lopez and Burreau 2018), we analyzed the distribution and expression pattern of these genes. Expression analyses were extended to all other genes harboring NIRVS (AALF025779 with AlbRha9, AALF000476 with AlbRha15, AALF000477 with AlbRha18 and AALF004130 with AlbRha85) that are fixed within the Foshan strain, but have LoP levels comparable to or lower than those of conserved genes (supplementary table S1).…”

Section: Resultsmentioning

confidence: 99%

Evolutionary landscape of mosquito viral integrations

Pischedda

Scolari

Valerio

et al. 2018

Preprint

View full text Add to dashboard Cite

The sequenced genome of the arboviral vector mosquito, Aedes albopictus, is replete with repetitive DNA and it harbors an unusually large number of endogenous viral sequences, collectively called Nonretroviral Integrated RNA Virus Sequences (NIRVS). NIRVS are enriched both within protein-coding gene exons and PIWI-interacting RNA (piRNA) clusters, where they encode piRNAs. Based on these features, NIRVS have been proposed to function as novel mosquito antiviral immune factors. However, the relative importance and contributions of different NIRVS as functional antiviral elements and their mechanisms of action remain open questions.We apply an analytical approach that intersects computational, evolutionary and molecular methods to identify NIRVS most likely affecting mosquito immunity. Using this strategy, we show that NIRVS are a highly dynamic component of the Ae. albopictus repeatome, which nevertheless maintains a core set of seemingly the oldest NIRVS with similarity to Rhabdoviruses. Population-level polymorphism of NIRVS varies depending on whether they occur in intergenic regions, piRNA clusters or are part of gene exons. NIRVS from piRNA clusters are differentially widespread in diverse populations but conserved at the sequence level. This is consistent with the hypothesis that they act analogously to fragments of transposable elements in piRNA clusters and contribute to piRNA-based immunity. Among NIRVS from gene exons, AlbRha52 and AlbRha12 have the hallmarks of domestication as they are fixed across populations, stably expressed, and as polymorphic at the sequence level as fast-evolving genes. Overall these results support the hypothesis that NIRVS contribute to mosquito immunity, potentially through diverse modes of action.

show abstract

Exaptation of transposable element coding sequences

Cited by 60 publications

References 60 publications

Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation

Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation

The soursop genome and comparative genomics of basal angiosperms provide new insights on evolutionary incongruence

Evolutionary landscape of mosquito viral integrations

Contact Info

Product

Resources

About