52fbdabe-74e5-4912-ba6f-3d63d11bf91a
Whole genome sequence read data from British oaks in the Forest Condition Survey
Whole genome sequences from 426 British oak trees. Trees were from 58 sites from the Forest Research Forest Condition Survey, funded by the Forestry Commission, and 2 sites from Forest Research FPPH study. Whole genome sequencing was carried out on the samples plus 14 technical replicates and the data delivered to RBG Kew for analysis. The data will be used to study the origins and population structure of British oaks as well as the relationship between genotypes and environmental variables or health conditions. Sequencing was funded by DEFRA Future Proofing Plant Health. Extraction, library preparation and sequencing was carried out by Novogene who established a bespoke extraction protocol based on the EchoLUTION Plant DNA 96 Core Kit protocol. Quality control was carried out using Agarose gel electrophoresis and Cubit 2.0 quantification. For library preparation, the genomic DNA was randomly fragmented by sonication, then DNA fragments were end polished, A-tailed, and ligated with the full-length adapters of Illumina sequencing. This was followed by further PCR amplification with P5 and indexed P7 oligos. The PCR were purified with AMPure XP system. For quality control, the libraries were checked for size distribution by Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), and quantified by real-time PCR (to meet the criteria of 3 nM). Libraries were sequenced on the Illumina Novaseq 6000 platform. Sequences were quality control filtered for adapter reads, reads where more than 10% of bases could not be determined and reads where over 50% of bases had a low quality score.
Whole genome sequences from 426 British oak trees. Trees were from 58 sites from the Forest Research Forest Condition Survey, funded by the Forestry Commission, and 2 sites from Forest Research FPPH study. Whole genome sequencing was carried out on the samples plus 14 technical replicates and the data delivered to RBG Kew for analysis. The data will be used to study the origins and population structure of British oaks as well as the relationship between genotypes and environmental variables or health conditions. Sequencing was funded by DEFRA Future Proofing Plant Health. Extraction, library preparation and sequencing was carried out by Novogene who established a bespoke extraction protocol based on the EchoLUTION Plant DNA 96 Core Kit protocol. Quality control was carried out using Agarose gel electrophoresis and Cubit 2.0 quantification. For library preparation, the genomic DNA was randomly fragmented by sonication, then DNA fragments were end polished, A-tailed, and ligated with the full-length adapters of Illumina sequencing. This was followed by further PCR amplification with P5 and indexed P7 oligos. The PCR were purified with AMPure XP system. For quality control, the libraries were checked for size distribution by Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), and quantified by real-time PCR (to meet the criteria of 3 nM). Libraries were sequenced on the Illumina Novaseq 6000 platform. Sequences were quality control filtered for adapter reads, reads where more than 10% of bases could not be determined and reads where over 50% of bases had a low quality score.