Computational protocol: Companion cropping with potato onion enhances the disease resistance of tomato against Verticillium dahliae

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Protocol publication

[…] Primary sequencing data (called raw reads) produced by Illumina HiSeq™ 2000 were cleaned by discarding reads with adapters and reads in which unknown bases are more than 10%. Low quality reads (sequencing quality is no more than 5) were removed as well. BWA (Li and Durbin, ) was used to map clean reads to tomato genome reference, and Bowtie (Langmead et al., ) to gene reference using the default parameters, respectively. Genes expression levels in terms of transcripts were quantified by RSEM (RNASeq by Expectation Maximization) and FPKM (Fragment Per Kilobase of exon model per Million mapped reads) method (Li and Dewey, ). The FPKM between the biological replications was analyzed by Pearson correlation. In our study, the Pearson coefficient of gene expression in different replications was more than 0.85, indicating the consistency between the replicates (Additional file 2: Figure ). According to the studies by Tarazonz et al., the Noiseq method was selected to screen differential expressed genes (DEGs) between group TM and TC, with diverge probability (PNOI) ≥ 0.8 and the absolute value of fold change ≥ 2 (log2Ratio≥1) as the threshold value (Tarazona et al., ). The expression patter analysis of DEGs is performed with cluster and java Treeview software. WEGO was used to classify GO function (Ye et al., ). Kyoto Encyclopedia of Genes and Genomes (KEGG), the major public pathway-related database, is used to perform pathway enrichment analysis of DEGs with Q ≤ 0.05 as significantly enriched threshold (Kanehisa et al., ). […]

Pipeline specifications

Software tools BWA, Bowtie, RSEM, NOISeq, TreeView, WEGO
Databases KEGG
Application RNA-seq analysis
Organisms Solanum tuberosum, Allium cepa, Solanum lycopersicum, Verticillium dahliae
Diseases Infection