Furthermore, we classified 19,715 (11.40 %) unigenes into 274 KEGG pathways by searching against the KEGG database (Additional file 3: Table S2). Among these pathways, “metabolic pathways”(3684, 18.7 %) represented the largest group, followed by “biosynthesis of secondary metabolites”(1616, 8.2 %). The other highly represented pathways included “microbial metabolism in diverse environment (803, 4.1 %)”, “ribosome (509, 2.6 %)” and “protein processing in endoplasmic reticulum (507, 2.6 %)” (Table 4). A total of 301 unigenes involved in plant hormone signal transduction were found, including 9 pathways controlling the signal transduction of auxin, cytokinin, gibberellin acid, abscisic acid, ethylene, brassinosteroid, jasmonic acid and salicylic acid (Table 5). Besides, through the KEGG pathway annotation, a circadian rhythm pathway including 58 unigenes was also found, which can be used for further studies on the flowering-related genes of the photoperiod pathway.Table 4Significantly enriched pathways of all unigenes and DEGs in C. faberi PathwayNo. of all genes with pathway annotation (19,715)No. of DEGs with pathway annotation (66)Pathway IDUp-regulated genesDown-regulat-ed genesMetabolic pathways368160240ko01100Biosynthesis of secondary metabolites161666186ko01110Microbial metabolism in diverse environments8034696ko01120Ribosome5091871ko03010Protein processing in endoplasmic reticulum5071448ko04141Spliceosome4692717ko03040RNA transport4572121ko03013Starch and sucrose metabolism4031248ko00500Cell cycle355258ko04110Tuberculosis3371126ko05152Pyrimidine metabolism3301913ko00240RNA degradation327197ko03018 Table 5The pathways involved in plant hormone biosynthesisPathwayProductPathway IDUnigene numberCysteine and methionine metabolismEthyleneko00270125Phenylalanine metabolismSalicylic acidko00360103Tryptophan metabolismAuxinko0038090alpha-Linolenic acid metabolismJasmonic acidko0059259Diterpenoid biosynthesisGibberellinko0090447Carotenoid biosynthesisAbscisic acidko0090628Zeatin biosynthesisCytokininko0090818Brassinosteroid biosynthesisBrassinosteroidko0090517Indole alkaloid biosynthesisIndole-acetic acidko009012