Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients

Molecular Ecology
Paul F GuggerVictoria L Sork

Abstract

DNA methylation in plants affects transposon silencing, transcriptional regulation and thus phenotypic variation. One unanswered question is whether DNA methylation could be involved in local adaptation of plant populations to their environments. If methylation alters phenotypes to improve plant response to the environment, then methylation sites or the genes that affect them could be a target of natural selection. Using reduced-representation bisulphite sequencing (RRBS) data, we assessed whether climate is associated with variation in DNA methylation levels among 58 naturally occurring, and species-wide samples of valley oak (Quercus lobata) collected across climate gradients. We identified the genomic context of these variants referencing a new draft valley oak genome sequence. Methylation data were obtained for 341 107 cytosines, of which we deemed 57 488 as single-methylation variants (SMVs), found in the CG, CHG and CHH sequence contexts. Environmental association analyses revealed 43 specific SMVs that are significantly associated with any of four climate variables, the majority of which are associated with mean maximum temperature. The 43 climate-associated SMVs tend to occur in or near genes, several of which have know...Continue Reading

References

Jun 24, 1997·Proceedings of the National Academy of Sciences of the United States of America·J K OkamuroK D Jofuku
Mar 1, 2003·The Plant Journal : for Cell and Molecular Biology·Joseph G DubouzetKazuko Yamaguchi-Shinozaki
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
May 22, 2007·The Plant Cell·So-Yon ParkNam-Chon Paek
Dec 17, 2009·The New Phytologist·Koen J F VerhoevenArjen Biere
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Feb 10, 2010·Nature Reviews. Genetics·Julie A Law, Steven E Jacobsen
Mar 23, 2011·Plant Science : an International Journal of Experimental Plant Biology·Igor A YakovlevØystein Johnsen
Mar 25, 2011·Methods in Molecular Biology·Suhua FengMatteo Pellegrini
May 10, 2011·Bioinformatics·Brian Walenz, Liliana Florea
Jun 28, 2011·Molecular Plant·Thomas K UthupSaha Thakurdas
Aug 5, 2011·Molecular Biology and Evolution·Shohei Takuno, Brandon S Gaut
Jun 27, 2012·Proceedings of the National Academy of Sciences of the United States of America·Robert H DowenJoseph R Ecker
Jul 11, 2012·Proceedings of the National Academy of Sciences of the United States of America·Ramakrishna K ChodavarapuMatteo Pellegrini
Jul 13, 2012·Genome Biology·Yaping LiuBenjamin P Berman
Sep 1, 2012·Annual Review of Genetics·Steven J Franks, Ary A Hoffmann
Sep 4, 2012·Current Opinion in Plant Biology·Claude Becker, Detlef Weigel
Sep 4, 2012·Trends in Ecology & Evolution·Liza M HoleskiAnurag A Agrawal
Nov 6, 2012·The New Phytologist·Yuan-Ye ZhangOliver Bossdorf
Feb 19, 2013·Nature Reviews. Genetics·Ueli GrossniklausSusan Lindquist
Feb 27, 2013·Nature Reviews. Genetics·Jae Hoon Sul, Eleazar Eskin
Mar 8, 2013·Nature·Robert J SchmitzJoseph R Ecker
Mar 8, 2013·Ecology and Evolution·Katharina BräutigamMaría-Teresa Cervera
Apr 13, 2013·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Filippos D KlironomosSinéad Collins
Jun 29, 2013·Trends in Genetics : TIG·Qiong A Liu
Oct 31, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Nicolas WidmanMatteo Pellegrini
Nov 12, 2013·BMC Genomics·Weilong GuoMatteo Pellegrini
Jan 21, 2014·Genetics·Jeremy B YoderPeter Tiffin
Feb 8, 2014·Science·Sandra CortijoFrank Johannes

❮ Previous
Next ❯

Citations

Mar 20, 2016·Molecular Ecology·Koen J F VerhoevenVictoria L Sork
Nov 9, 2016·Frontiers in Genetics·Amy V Whipple, Liza M Holeski
Feb 6, 2017·Molecular Ecology·Alejandra Rodríguez-VerdugoJessica Stapley
Jun 10, 2017·Journal of Evolutionary Biology·J Hu, R D H Barrett
Apr 17, 2018·Genome Génome / Conseil National De Recherches Canada·Shruti ChoudharyPankaj Bhardwaj
May 16, 2018·Omics : a Journal of Integrative Biology·Nina Pirih, Tanja Kunej
Oct 14, 2017·Ecology Letters·Christina L RichardsKoen J F Verhoeven
Oct 19, 2017·The Journal of Heredity·Victoria L Sork
Sep 14, 2016·G3 : Genes - Genomes - Genetics·Victoria L SorkSteven L Salzberg
Jun 30, 2018·BMC Genomics·Elizabeth S A Sollars, Richard J A Buggs
Aug 26, 2017·Interface Focus·Sonia E Sultan
Jul 25, 2019·Molecular Ecology·Sofia J van MoorselPhilippine Vergeer
Nov 12, 2019·Molecular Ecology·Guinevere O U WoganIan J Wang
Sep 19, 2019·Journal of Evolutionary Biology·Mark W SmithsonScott L Nuismer
Apr 1, 2020·Molecular Biology and Evolution·Kostas SagonasChristophe Eizaguirre
Aug 25, 2017·BMC Evolutionary Biology·Sabrina M McNewMichael K Skinner
Nov 5, 2019·Molecular Ecology Resources·Tricia L RubiBen Dantzer
Nov 6, 2018·Ecology and Evolution·Katrin HeerStefan A Rensing
Dec 12, 2018·Proceedings of the National Academy of Sciences of the United States of America·Groves DixonMikhail V Matz
Jan 9, 2019·Frontiers in Plant Science·Gerald A TuskanJoshua K Michener
May 14, 2019·Plant Biology·M Müller, O Gailing
May 30, 2020·Integrative and Comparative Biology·Beth A McCawLesley T Lancaster
May 23, 2018·Nature Reviews. Molecular Cell Biology·Huiming ZhangJian-Kang Zhu
Nov 21, 2017·Evolutionary Applications·Marta RobertsonChristina Richards
Jul 28, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Mariana Villalba de la PeñaReinmar Hager
Oct 20, 2017·Nature Ecology & Evolution·Amanda J LeaJenny Tung
Oct 6, 2020·Frontiers in Plant Science·Alexander JueterbockGalice Hoarau
Jan 17, 2020·G3 : Genes - Genomes - Genetics·Luke BrowneVictoria L Sork

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.