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 (Co-auteur), Koen J. F. Verhoeven, Christina L. Richards

NIOO - Terrestrial Ecology (TE)

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

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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.

Originele taal-2	Engels
Pagina's (van-tot)	738-742
Tijdschrift	New Phytologist
Volume	221
Nummer van het tijdschrift	2
DOI's	https://doi.org/10.1111/nph.15388
Status	Gepubliceerd - jan. 2019

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10.1111/nph.15388Licentie: Other

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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.",

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

author = "Ovidiu Paun and Verhoeven, {Koen J. F.} and Richards, {Christina L.}",

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Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics. / Paun, Ovidiu (Co-auteur); Verhoeven, Koen J. F.; Richards, Christina L.
In: New Phytologist, Vol. 221, Nr. 2, 01.2019, blz. 738-742.

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

TY - JOUR

T1 - Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics

AU - Paun, Ovidiu

AU - Verhoeven, Koen J. F.

AU - Richards, Christina L.

N1 - 6683, TE; Data Archiving: no data review

PY - 2019/1

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N2 - 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.

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

U2 - 10.1111/nph.15388

DO - 10.1111/nph.15388

M3 - Article

SN - 0028-646X

VL - 221

SP - 738

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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