aligned using the KOG (Eukaryotic Orthologous Groups) database to predict and classify their functions (Grabherr et al., 2011).
Candidate gene pathways were identified and annotated using Kyoto encyclopedia of genes and genomes (KEGG, http://www.genome.jp/kegg/pathway.html) pathway software, KOBAS v. 2.0 (Xie et al., 2011).
Differentially expressed genes (DEGs)
The expression level for each transcript was calculated using the fragments per kilobase of exon per million mapped reads method to identify
Journal of Nematology , 1–14
analyzed using OrthoVenn2 with default options (Xu et al., 2019).
Differentially expressed genes (DEGs) analyses and GO enrichment analysis of DEGs
For DEG analyses, complete FPKM and edgeR scores were taken, and the statistical significance (P value and Q value) and fold changes (FC) were calculated, based on the normalized values. The filter cut-offs (i.e., P ≤ 0.05, Q ≤ 0.05 and FC ≥ 2) were used to select the DEGs/transcripts from the given pairs. Gene Ontology (GO) terms for the identified genes
Journal of Nematology , 1–16