Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics

Ovidiu Paun; Koen J. F. Verhoeven; Christina L. Richards

doi:10.1111/nph.15388

Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics

Ovidiu Paun (Corresponding author), Koen J. F. Verhoeven, Christina L. Richards

NIOO - Terrestrial Ecology (TE)

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Abstract

Investigating the features and implications of epigenetic mechanisms across the breadth of organisms and ecosystems is important for understanding the ecological relevance of epigenetics. Several cost-effective reduced representation bisulfite sequencing approaches (RRBS) have been recently developed and applied to different organisms that lack a well annotated reference genome. These new approaches improve the assessment of epigenetic diversity in ecological settings and may provide functional insights. We assess here the opportunities and limitations of RRBS in nonmodel plant species. Well thought out experimental designs that include complementary gene expression studies, and the improvement of genomics resources for the target group, promise to maximize the effect of future RRBS studies.

Original language	English
Pages (from-to)	738-742
Journal	New Phytologist
Volume	221
Issue number	2
DOIs	https://doi.org/10.1111/nph.15388
Publication status	Published - Jan 2019

Keywords

international
bsRADseq
DNA methylation
ecological genomics
epiGBS
reduced representation bisulfite sequencing (RRBS)
response to environment
adaptation
bisulfite sequencing

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abstract = "Investigating the features and implications of epigenetic mechanisms across the breadth of organisms and ecosystems is important for understanding the ecological relevance of epigenetics. Several cost-effective reduced representation bisulfite sequencing approaches (RRBS) have been recently developed and applied to different organisms that lack a well annotated reference genome. These new approaches improve the assessment of epigenetic diversity in ecological settings and may provide functional insights. We assess here the opportunities and limitations of RRBS in nonmodel plant species. Well thought out experimental designs that include complementary gene expression studies, and the improvement of genomics resources for the target group, promise to maximize the effect of future RRBS studies.",

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AU - Paun, Ovidiu

AU - Verhoeven, Koen J. F.

AU - Richards, Christina L.

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AB - Investigating the features and implications of epigenetic mechanisms across the breadth of organisms and ecosystems is important for understanding the ecological relevance of epigenetics. Several cost-effective reduced representation bisulfite sequencing approaches (RRBS) have been recently developed and applied to different organisms that lack a well annotated reference genome. These new approaches improve the assessment of epigenetic diversity in ecological settings and may provide functional insights. We assess here the opportunities and limitations of RRBS in nonmodel plant species. Well thought out experimental designs that include complementary gene expression studies, and the improvement of genomics resources for the target group, promise to maximize the effect of future RRBS studies.

KW - international

KW - bsRADseq

KW - DNA methylation

KW - ecological genomics

KW - epiGBS

KW - reduced representation bisulfite sequencing (RRBS)

KW - response to environment

KW - adaptation

KW - bisulfite sequencing

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DO - 10.1111/nph.15388

M3 - Article

SN - 0028-646X

VL - 221

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EP - 742

JO - New Phytologist

JF - New Phytologist

IS - 2

ER -

Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics

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Keywords

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