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[…] ulation of the six different plum types studied in this work have previously been described (Minas et al., )., Genomic DNA of the six cultivars was isolated from leaves using standard Cetyl Trimethylammonium Bromide (CTAB) methods (Lodhi et al., ). Five micro gramstotal gDNA was sheared to a fragment size of ~600 bp with a Covaris ultrasonicator (Aubakirova et al., ) and Illumina-ready sequencing libraries were prepared using the Illumina TruSeq-DNA library preparation kit, following the manufacturer's recommended procedures. WGS sequences were collected on an Illumina HiSeq2500 using a 2 × 125 bp paired-end module., After sequencing, raw sequence reads were subject to quality analysis with FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and pre-processed to remove low-quality bases and adapter sequences with the Trimmomatic tool (Bolger et al., ). Pre-processed sequence reads were aligned to the Prunus persica (Verde et al., ) reference genome assembly v. 2.0 using the Bowtie2 short read aligner tool (Langmead and Salzberg, ). Gene CNV was performed with a sliding window of 100 bp and the CNVnator prediction algorithm (Abyzov et al., ). CNVnator output was converted to tabular format with in-house scripts and combined with the peach gene annotation files for analysis of genes. Coding variations (SNPs and INDELS), both relative to peach and among the plum samples, were determined with UnifiedGenotyper, a genotyping walker in the Genome Analysis Tool Kit (DePristo et al., ) with output in vcf format. Variants were filtered for depth (DP5) and mapping quality (MQ30), using in-house scripts. Functional annotations of mutations were determined with the SNPeff and SNPsift software tools (Cingolani et al., ). Variant sites were removed where all six plum varieties shared the same genotype, creating a final variant file output that contains sites where at least one variety differs from the other five using in-house scripts (Supplementary Table , ). Relative SNP densities were determined using a 100 kb window and plotted using the Circos plotting tool (Krzywinski et al., )., Predicted proteome sequences from Citrus clementine, Solanum lycopersicum, Fragaria vesca, Malus domestica, Arabidopsis thaliana, Vitis vinifera, P. persica, Pinus taeda, and Carica papaya were selected and downloaded from phytozome (https://phytozome.jgi.doe.gov/pz/portal.html). The interProScan 4-package software (https://www.ebi.ac.uk/interpro/) was used to identify the proteins in each proteome dataset. Local databases for each included plant species were developed to allow us to extract and interpret the large amount of data obtained in this study. Out of all loci identified, nine for ethylene and two for sorbitol responses were clearly diffe […]

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