Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spann...

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Autores principales:	Federico Rossi, Alessandro Crnjar, Federico Comitani, Rodrigo Feliciano, Leonie Jahn, George Malim, Laura Southgate, Emily Kay, Rebecca Oakey, Richard Buggs, Andy Moir, Logan Kistler, Ana Rodriguez Mateos, Carla Molteni, Reiner Schulz
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2693f679d5b74116945a1b30943a6d32
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spelling	oai:doaj.org-article:2693f679d5b74116945a1b30943a6d322021-11-25T06:19:39ZExtraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling1932-6203https://doaj.org/article/2693f679d5b74116945a1b30943a6d322021-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601515/?tool=EBIhttps://doaj.org/toc/1932-6203Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus robur) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.Federico RossiAlessandro CrnjarFederico ComitaniRodrigo FelicianoLeonie JahnGeorge MalimLaura SouthgateEmily KayRebecca OakeyRichard BuggsAndy MoirLogan KistlerAna Rodriguez MateosCarla MolteniReiner SchulzPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Federico Rossi Alessandro Crnjar Federico Comitani Rodrigo Feliciano Leonie Jahn George Malim Laura Southgate Emily Kay Rebecca Oakey Richard Buggs Andy Moir Logan Kistler Ana Rodriguez Mateos Carla Molteni Reiner Schulz Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling
description	Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus robur) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.
format	article
author	Federico Rossi Alessandro Crnjar Federico Comitani Rodrigo Feliciano Leonie Jahn George Malim Laura Southgate Emily Kay Rebecca Oakey Richard Buggs Andy Moir Logan Kistler Ana Rodriguez Mateos Carla Molteni Reiner Schulz
author_facet	Federico Rossi Alessandro Crnjar Federico Comitani Rodrigo Feliciano Leonie Jahn George Malim Laura Southgate Emily Kay Rebecca Oakey Richard Buggs Andy Moir Logan Kistler Ana Rodriguez Mateos Carla Molteni Reiner Schulz
author_sort	Federico Rossi
title	Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling
title_short	Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling
title_full	Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling
title_fullStr	Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling
title_full_unstemmed	Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling
title_sort	extraction and high-throughput sequencing of oak heartwood dna: assessing the feasibility of genome-wide dna methylation profiling
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/2693f679d5b74116945a1b30943a6d32
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Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling

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