epiGBS: reference-free reduced representation bisulfite sequencing

Gurp, Thomas P. van; Wagemaker, Cornelis A. M.; Wouters, B.; Vergeer, Philippine; Ouborg, Joop; Verhoeven, Koen J. F.

doi:10.1038/nmeth.3763

Cited by 121 publications

(163 citation statements)

References 21 publications

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“…In future studies, a reduced‐representation bisulfite sequencing approach would allow the direct comparison of genetic and epigenetic data sets, and at a much finer scale, with substantially increased statistical power to detect epigenetic differences between populations (van Gurp et al., 2016; Robertson & Richards, 2015; Schrey et al., 2013; Trucchi et al., 2016). In addition, sequencing‐based methods provide an increased ability to disentangle the relationship of methylation variation and gene function when fragments overlap with the promoters or coding regions of genes.…”

Section: Discussionmentioning

confidence: 99%

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

Robertson

Schrey

Shayter

et al. 2017

Evolutionary Applications

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Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation sensitive fragment length polymorphism (MS‐AFLP) to test the hypothesis that response to oil exposure in S. alterniflora resulted in genetically and epigenetically based population differentiation. We found high genetic and epigenetic variation within and among sites and found significant genetic differentiation between contaminated and uncontaminated sites, which may reflect nonrandom mortality in response to oil exposure. Additionally, despite a lack of genomewide patterns in DNA methylation between contaminated and uncontaminated sites, we found five MS‐AFLP loci (12% of polymorphic MS‐AFLP loci) that were correlated with oil exposure. Overall, our findings support genetically based differentiation correlated with exposure to the oil spill in this system, but also suggest a potential role for epigenetic mechanisms in population differentiation.

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Section: Discussionmentioning

confidence: 99%

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

Robertson

Schrey

Shayter

et al. 2017

Evolutionary Applications

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“…To assess differential methylation levels in TE sequences among accessions, we used a recently developed reduced representation bisulfite sequencing (RRBS) protocol that does not require a reference genome [40]. Individuals originating from the same mother plants as the ones used for genomic sequencing were grown in a common greenhouse environment.…”

Section: Methodsmentioning

confidence: 99%

Recent and dynamic transposable elements contribute to genomic divergence under asexuality

et al. 2016

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BackgroundTransposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptive genetic variation. This additional source of variation could be especially relevant in non-recombining species reproducing asexually. However, evidence is lacking to determine the relevance of TEs in plant asexual genome evolution and their associated effects. Here, we characterize the repetitive fraction of the genome of the common dandelion, Taraxacum officinale and compare it between five accessions from the same apomictic lineage. The main objective of this study is to evaluate the extent of within-lineage divergence attributed to TE content and activity. We examined the repetitive genomic contribution, diversity, transcription and methylation changes to characterize accession-specific TEs.ResultsUsing low-coverage genomic sequencing, we report a highly heterogeneous TE compartment in the triploid apomict T. officinale representing up to 38.6 % of the homoploid genome. The repetitive compartment is dominated by LTR retrotransposon families accompanied by few non-LTR retrotransposons and DNA transposons. Up to half of the repeat clusters are biased towards very high read identity, indicating recent and potentially ongoing activity of these TE families. Interestingly, the five accessions are divided into two main clades based on their TE composition. Clade 2 is more dynamic than clade 1 with higher abundance of Gypsy Chromovirus sequences and transposons. Furthermore, a few low-abundant genomic TE clusters exhibit high level of transcription in two of the accessions analysed. Using reduced representation bisulfite sequencing, we detected 18.9 % of loci differentially methylated, of which 25.4 and 40.7 % are annotated as TEs or functional genes, respectively. Additionally, we show clear evidence for accession-specific TE families that are differentially transcribed and differentially methylated within the apomictic lineage, including one Copia Ale II LTR element and a PIF-Harbinger DNA transposon.ConclusionWe report here a very young and dynamic repetitive compartment that enhances divergence within one asexual lineage of T. officinale. We speculate that accession-specific TE families that are both transcriptionally and epigenetically variable are more prone to trigger changes in expression on nearby coding sequences. These findings emphasize the potential of TE-induced mutations on functional genes during asexual genome evolution.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3234-9) contains supplementary material, which is available to authorized users.

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“…Bisulfite sequencing is considered the 'gold-standard' to characterize DNA-methylation as the only method resolving nucleotide-level polymorphisms (Schrey et al, 2013;Adusumalli et al, 2014). While whole genome bisulfite sequencing is still expensive for large sample sizes, reduced representation techniques, such as RRBS (Gu et al, 2011), bsRADseq (Trucchi et al, 2016), and epiGBS (van Gurp et al, 2016) allow for cost-effective population epigenetic comparisons, partly without the need for a reference genome. Alternatively, DNA-methylation can be characterized with markers obtained via methylation-sensitive restriction enzymes, such as EpiRAD (Schield et al, 2016) and MethylRAD (Wang et al, 2015).…”

Section: A2 Epigenetic Potential To Adapt To Climate Changementioning

confidence: 99%

Climate Change Impacts on Seagrass Meadows and Macroalgal Forests: An Integrative Perspective on Acclimation and Adaptation Potential

et al. 2018

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Marine macrophytes are the foundation of algal forests and seagrass meadows-some of the most productive and diverse coastal marine ecosystems on the planet. These ecosystems provide nursery grounds and food for fish and invertebrates, coastline protection from erosion, carbon sequestration, and nutrient fixation. For marine macrophytes, temperature is generally the most important range limiting factor, and ocean warming is considered the most severe threat among global climate change factors. Ocean warming induced losses of dominant macrophytes along their equatorial range edges, as well as range extensions into polar regions, are predicted and already documented. While adaptive evolution based on genetic change is considered too slow to keep pace with the increasing rate of anthropogenic environmental changes, rapid adaptation may come about through a set of non-genetic mechanisms involving the functional composition of the associated microbiome, as well as epigenetic modification of the genome and its regulatory effect on gene expression and the activity of transposable elements. While research in terrestrial plants demonstrates that the integration of non-genetic mechanisms provide a more holistic picture of a species' evolutionary potential, research in marine systems is lagging behind. Here, we aim to review the potential of marine macrophytes to acclimatize and adapt to major climate change effects via intraspecific variation at the genetic, epigenetic, and microbiome levels. All three levels create phenotypic variation that may either enhance fitness within individuals (plasticity) or be subject to selection and ultimately, adaptation. We

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epiGBS: reference-free reduced representation bisulfite sequencing

Cited by 121 publications

References 21 publications

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

Recent and dynamic transposable elements contribute to genomic divergence under asexuality

Climate Change Impacts on Seagrass Meadows and Macroalgal Forests: An Integrative Perspective on Acclimation and Adaptation Potential

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