PMID- 30121954
OWN - NLM
STAT- MEDLINE
DCOM- 20200114
LR  - 20231011
IS  - 1469-8137 (Electronic)
IS  - 0028-646X (Print)
IS  - 0028-646X (Linking)
VI  - 221
IP  - 2
DP  - 2019 Jan
TI  - Opportunities and limitations of reduced representation bisulfite sequencing in 
      plant ecological epigenomics.
PG  - 738-742
LID - 10.1111/nph.15388 [doi]
AB  - Contents Summary 738 I. Introduction 738 II. RRBS loci as genome-wide epigenetic 
      markers 739 III. Exploiting functional annotation of RRBS loci 739 IV. 
      Limitations of RRBS methods for nonmodel species 740 V. Maximising the impact of 
      RRBS in plants 741 VI. Conclusions 741 Acknowledgements 741 SUMMARY: 
      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.
CI  - (c) 2018 The Authors. New Phytologist (c) 2018 New Phytologist Trust.
FAU - Paun, Ovidiu
AU  - Paun O
AUID- ORCID: 0000-0002-8295-4937
AD  - Department for Botany and Biodiversity Research, University of Vienna, Vienna, 
      1030, Austria.
FAU - Verhoeven, Koen J F
AU  - Verhoeven KJF
AUID- ORCID: 0000-0003-3002-4102
AD  - Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands.
FAU - Richards, Christina L
AU  - Richards CL
AUID- ORCID: 0000-0001-7848-5165
AD  - Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, 
      USA.
LA  - eng
GR  - Y 661/FWF_/Austrian Science Fund FWF/Austria
GR  - 764965/Marie Sklodowska-Curie/International
GR  - Y661-B16/Austrian Science Fund/International
GR  - IOS-1556820/National Science Foundation/International
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PT  - Review
DEP - 20180819
PL  - England
TA  - New Phytol
JT  - The New phytologist
JID - 9882884
RN  - 0 (Sulfites)
RN  - OJ9787WBLU (hydrogen sulfite)
SB  - IM
MH  - *Ecological and Environmental Phenomena
MH  - Epigenomics/*methods
MH  - Molecular Sequence Annotation
MH  - Plants/*genetics
MH  - Sequence Analysis, DNA/*methods
MH  - Sulfites/*chemistry
PMC - PMC6504643
MID - EMS82368
OTO - NOTNLM
OT  - DNA methylation
OT  - adaptation
OT  - bisulfite sequencing
OT  - bsRADseq
OT  - ecological genomics
OT  - epiGBS
OT  - reduced representation bisulfite sequencing (RRBS)
OT  - response to environment
EDAT- 2018/08/20 06:00
MHDA- 2020/01/15 06:00
PMCR- 2019/05/08
CRDT- 2018/08/20 06:00
PHST- 2018/04/22 00:00 [received]
PHST- 2018/07/03 00:00 [accepted]
PHST- 2018/08/20 06:00 [pubmed]
PHST- 2020/01/15 06:00 [medline]
PHST- 2018/08/20 06:00 [entrez]
PHST- 2019/05/08 00:00 [pmc-release]
AID - 10.1111/nph.15388 [doi]
PST - ppublish
SO  - New Phytol. 2019 Jan;221(2):738-742. doi: 10.1111/nph.15388. Epub 2018 Aug 19.