Project description:Acute Oak Decline (AOD) is a decline-disease currently spreading in Britain, threatening oak trees. Here, we analyze and compare the proteomes of inner bark tissue sampled from oak stems of trees symptomatic with AOD and non-symptomatic trees.
Project description:The transcriptome of Phanerochaete chrysosporium control mycelium was compared to the transcriptome of mycelium grown on oak acetonic extractives containing medium. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Phanerochaete chrysosporium genome sequence version 1. The aim of this study was to determine gene expression changes in Phanerochaete chrysosporium grown on oak extract with a special focus on detoxification systems.
Project description:Expression diversity of P. ramorum isolates belonging to the NA1 clonal lineage growing on solid CV8 was examined. We found that phenotypes and transcriptomes change when isolates were passing through oak trees.
Project description:Iso-Seq "full length" transcript sequences were used as one of many guides informing gene model annotation of the Valley Oak genome sequence.
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.
Project description:Illumina HiSeq2500 technology was used to generate mRNA profiles from Phanerochaete chrysosporium treated with oak extractives for 1, 3 and 6h. 125bp pair-end reads were generated and aligned to the P.chrysosporium reference transcripts. (https://genome.jgi.doe.gov/Phchr2/Phchr2.home.html) using CLC Genomics Workbench 9.
