biostudies-arrayexpressMarkus KuhlmannSolanum tuberosumBismark , bowtie2, samtools , qualimap packageFastQC, Trim-Galorehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15777DNA methylation is an epigenetic mark that can be transmitted from one generation to the next. DNA methylation patterns can be specific to environmental conditions. In our ap-proach, differences in DNA methylation pattern were compared among tubers of potato (Solanum tuberosum) grown under organic and conventional farming conditions. These conditions differed in application of fertilizer, herbicides, fungicides and insecticides. Samples grown at two different years under organic and conventional growing conditions in three independent field replicates were analyzed to identify differentially methylated regions (DMRs). Post-bisulfite-adapter tagging whole-genome bisulfite-sequencing (PBAT-WGBS) was performed on the extracted DNA. Only using relaxed selection param-eters revealed sixty shared DMRs were identified among both years analyzed. One of the identified DMR was associated with the StATOX1 gene. StATOX1 is an evolutionarily highly conserved antioxidant copper chaperone, responsible for detoxification of copper in organisms. Copper content of the potato samples was measured by Inductively-Coupled Plasma-Atomic-Emission-Spectrometry (ICP-AES) after high pressure nitric acid oxidation. As organic potato management relies on the application of copper as fungicide, our iden-tified region might be indicative for the application of this specific compound.biostudies-arrayexpressSequencing - Library preparation and sequencing was performed at Novogene Inc. (Novogene Co., Ltd. Novogene Biotech Co., Ltd. Building 301, Zone A10 Jiuxianqiao North Road, Chao-yang District, Beijing). After transfer of samples integrity, quantity and quality of DNA was controlled. Afterwards the DNA has been sheared using Covaris S220 to fragments of 200-400 bp and further processed according the library preparation protocol including terminal repair, A-ligation and ligation of sequencing adapters. HiSeq X Ten (Illumina Inc., 9885 Towne Centre Drive. San Diego, CA 92121 U.S.A.) sequencing, with paired-end 150 bp, including multiplexing of other, non-bisulfite treated, samples has been applied to account for the unbalanced base ratio in WGBS libraries. The effective concentration of the final library has been >2 nM. A Lambda Phi X spike-in with 0.5% of DNA weight has been applied as conversion standard. The demultiplexed raw data has been received.Nucleic Acid Extraction - column-based DNeasy kit according to manufacturer (Qiagen) protocol, including a first phenol purification step with 100 mg of the ground potato sample. Integrity of DNA was tested by gel electrophoresis and Ethidiumbromid stainingLibrary Construction - a Whole-Genome-Bisulfite Sequencing (WGBS) procedure using a Post-Bisulfite Adapt-er-Tagging protocol (PBAT) to account for low amounts of DNA using the EZ DNA Meth-ylation Gold-TM Kit, Zymo Research. DNA concentration after bisulfite conversion was quantified using Qubit and q-PCR.Sample Treatment - (D: bio-dynamic, O: bio-organic, K: conventional)Sample Collection - For the study DNA from potato tubers was used. The potato tubers (Solanum tuberosum var. Desirée) we harvested from the DOK-field trial (D: bio-dynamic, O: bio-organic, K: con-ventional) in Therwil, Switzerland of Agroscope, the Swiss Centre of Excellence for Agri-cultural Research and the Research Institute of Organic Agriculture (Foschungsinstitut für biologischen Landbau - FIBL). The DOK is one of the largest and the longest lasting long-term field trial of its kind, initiated in 1978. The samples have been kindly provided by Agroscope. Fully developed tubers (according BBCH Scale 909) were collected at harvest time (Hack et al. 1993) from potato plants (Solanum tuberosum cv. Desiree) in four replicates of the bio-organic cropping system (organic) and the conventional cropping system (conventional) from four years (2001, 2009, 2011, 2012). The complete tubers formed a representative sample of the plot per biological replicate.Growth Protocol - The potato tubers (Solanum tuberosum var. Desirée) we harvested from the DOK-field trial (D: bio-dynamic, O: bio-organic, K: conventional) in Therwil, Switzerland of Agroscope, the Swiss Centre of Excellence for Agricultural Research and the Research Institute of Organic Agriculture (Foschungsinstitut für biologischen Landbau - FIBL).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Remaining adapter and low quality sequences of the raw reads have been carefully analysed with FastQC (Leggett et al. 2013) and removed during trimming using Trim-Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) [--illumina –paired -q 20 --clip_r2 18 --clip_r1 7 --three_prime_clip_R1 18 --three_prime_clip_R2 3]. We appliedSequence Alignment - Bismark (Krueger and Andrews 2011) with bowtie2 (Langmead and Salzberg 2012) [--score_min L,0,-0.6 ] for mapping of each technical replicate separately including exten-sive quality check of the .bam files using samtools (Li et al. 2009), and bamqc from the qualimap package (García-Alcalde et al. 2012).UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq XBisulfite-seqSolanum tuberosumMarkus KuhlmannfalseAnalysis of Differences in DNA Methylation in Organically and Conventionally Grown Potato Tubers (Solanum tuberosum)DNA methylation is an epigenetic mark that can be transmitted from one generation to the next. DNA methylation patterns can be specific to environmental conditions. In our ap-proach, differences in DNA methylation pattern were compared among tubers of potato (Solanum tuberosum) grown under organic and conventional farming conditions. These conditions differed in application of fertilizer, herbicides, fungicides and insecticides. Samples grown at two different years under organic and conventional growing conditions in three independent field replicates were analyzed to identify differentially methylated regions (DMRs). Post-bisulfite-adapter tagging whole-genome bisulfite-sequencing (PBAT-WGBS) was performed on the extracted DNA. Only using relaxed selection param-eters revealed sixty shared DMRs were identified among both years analyzed. One of the identified DMR was associated with the StATOX1 gene. StATOX1 is an evolutionarily highly conserved antioxidant copper chaperone, responsible for detoxification of copper in organisms. Copper content of the potato samples was measured by Inductively-Coupled Plasma-Atomic-Emission-Spectrometry (ICP-AES) after high pressure nitric acid oxidation. As organic potato management relies on the application of copper as fungicide, our iden-tified region might be indicative for the application of this specific compound.2025-11-01T00:00:00Z2025-11-01T02:01:43.305Z2025-10-20T10:44:12.587ZE-MTAB-15777ERP182490EFO_0002944EFO_0004170EFO_0003789EFO_0003753EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969