Illumina RNA-seq Analysis of Silkworm

Quality analysis was conducted for the original data obtained using the Illumina HiSeqTM2500 system; after quality criteria were met, clean reads were screened by filtering out low-quality reads. The sequences were aligned to the silkworm genome database SilkDB (http://silkworm.swu.edu.cn/silkdb/); after a second quality analysis for alignment, analysis of the distribution and coverage of the clean reads on the reference sequence was conducted. RPKM (Reads Per Kb per Million reads) [24 (link)] was used to calculate the expression level of genes, with RPKM = mapped reads of gene/(the total mapped reads of all genes*the length of this gene)*10^9. The RPKM of a gene ranged up to 5, and difference in expression was considered at P < 0.05; the fold change of q-l^p and 932VR RPKMs was greater than 2. The function of the differentially expressed genes and pathways related to pigment were analyzed using BLASTGO and KEGG, respectively.