Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling.
Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling.
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DOI：
10.1371/journal.pone.0254971
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发表时间：
2021
期刊：
影响因子：
3.7
通讯作者：
Schulz R
中科院分区：
文献类型：
--
作者：
Rossi F;Crnjar A;Comitani F;Feliciano R;Jahn L;Malim G;Southgate L;Kay E;Oakey R;Buggs R;Moir A;Kistler L;Rodriguez Mateos A;Molteni C;Schulz R
树木年轮特征受环境因素的影响，因此是树木年代学研究重建过去环境条件的基础。橡木通常为这些研究提供数据，因为橡木心材的耐用性，因此可以获得跨越很长时间的样品。木材的形成部分受表观遗传机制如DNA甲基化的调控。因此，对保存在橡树心材中的DNA甲基化状态的研究可以确定表观遗传的树木年轮特征，从而为过去的环境条件提供信息。在这项研究中，我们的目的是建立DNA的提取，全基因组DNA文库（WGS）的高通量测序和DNA甲基化的全基因组亚硫酸氢盐测序（WGBS）的分析方案，从活的立木树干跨越AD 1776-2014时间段的橡树（栎）心材钻芯。心材含有很少的DNA和大量的酚类化合物，已知这些酚类化合物会阻碍高通量测序文库的制备。全基因组和DNA甲基化文库的制备和测序始终失败的橡木心材样品超过100年和50岁，分别。DNA片段化随着样品年龄的增加而增加，并且在甲基化组文库制备期间通过额外的亚硫酸氢盐处理步骤而加剧。橡树基因组的非重复部分的相对覆盖率是稀疏的。这些结果表明，橡木硬木的定量甲基化组研究可能仅限于相对较新的样品，并将需要高测序深度，以实现足够的基因组覆盖率。
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.
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影响因子：
4.1
作者：
Feliciano, Rodrigo P.;Mecha, Elsa;Rodriguez-Mateos, Ana
通讯作者：
Rodriguez-Mateos, Ana
影响因子：
14.8
作者：
Ainsworth, Elizabeth A.;Gillespie, Kelly M.
通讯作者：
Gillespie, Kelly M.
影响因子：
4.4
作者：
JOHNSTON, CG;AUST, SD
通讯作者：
AUST, SD
影响因子：
2.9
作者：
Bahnweg, G;Schulze, S;Sandermann, H
通讯作者：
Sandermann, H
影响因子：
48
作者：
Ivani I;Dans PD;Noy A;Pérez A;Faustino I;Hospital A;Walther J;Andrio P;Goñi R;Balaceanu A;Portella G;Battistini F;Gelpí JL;González C;Vendruscolo M;Laughton CA;Harris SA;Case DA;Orozco M
通讯作者：
Orozco M