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

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

PROVIDER: PRJNA599186 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10836600_1.fastq.gz	Fastqsanger.gz
	SRR10836600_2.fastq.gz	Fastqsanger.gz
	SRR10836601_1.fastq.gz	Fastqsanger.gz
	SRR10836601_2.fastq.gz	Fastqsanger.gz
	SRR10836602_1.fastq.gz	Fastqsanger.gz

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

Project 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 particularly 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 in the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. We investigated the feasibility of such studies using heartwood samples core-drilled from the trunks of standing oak trees spanning the AD 1776-2014. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. We sequenced whole-genome and DNA methylome libraries for oak heartwood up to 100 and 50 years of age, respectively. However, only 56 genomic regions with sufficient coverage for quantitative methylation analysis were identified, suggesting that the high-throughput sequencing of DNA will be in principal feasible for wood formed <100 years ago is impeded by the reduction in library complexity caused by the bisulfite treatment used to generate the oak methylome.

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

Project 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.

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