Received: JAccepted: OctoPublished: November 18, 2021Ĭopyright: © 2021 Rossi et al. (2021) Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling. 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.Ĭitation: Rossi F, Crnjar A, Comitani F, Feliciano R, Jahn L, Malim G, et al. Relative coverage of the non-repetitive portion of the oak genome was sparse. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries.
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. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. 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. These lines are already included in the example PBS scripts.Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. On Maple: export g16root=/usr/local/apps/gaussian/g16-c01-avx On Sequoia or Catalpa: export g09root=/usr/local/apps/ To run Gaussian interactively, or use its utility programs, first run: Unfortunately, there is no module for Gaussian due to the way it is setup.
Maple’s PBS tries to assign jobs to the newer nodes first, so jobs will generally end up on the newer nodes (AVX2) unless it requests lots of resources or the system is busy. Maple’s example job detects whether it is on an old node or new node and uses the appropriate version of Gaussian (AVX or AVX2). The example job for Maple can be found at /usr/local/apps/example_jobs/g16_maple_example. The Sequoia example job can be found at /usr/local/apps/example_jobs/g09_sequoia_example. Just run it without arguments for more information. On Sequoia and Catalpa there is a script called g09sub that will write a PBS script and submit it for you.
Unfortunately, the license to run a single Gaussian job across multiple nodes is quite expensive, so Gaussian jobs on our systems can only run on multiple cores on a single node.
The version currently installed will not run on Maple’s GPUs. Version 09 is installed on Sequoia and version 16 (Revision C.01) is installed on Maple. Gaussian is computational chemistry software that is most of our most popular software packages.