Identification and comparison of long non-coding RNAs in the silk gland between domestic and wild silkworms

Under long-term artificial selection, the domestic silkworm (Bombyx mori) has increased its silk yield tremendously in comparison with its wild progenitor, Bombyx mandarina. However, the molecular mechanism of silk yield increase is still unknown. Comparative analysis of long non-coding RNAs (lncRNAs) may provide some insights into understanding this phenotypic variation. In this study, using RNA sequencing technology data of silk gland in domestic and wild silkworms, we identified 599 lncRNAs in the silk gland of the silkworm. Compared with protein-coding genes, the silk gland lncRNA genes tend to have fewer exon numbers, shorter transcript length and lower GC-content. Moreover, we found that three lncRNA genes are significantly and differentially expressed between domestic and wild silkworms. The potential targets of two differentially expressed lncRNAs (DELs) (dw4sg_0040 and dw4sg_0483) and the expression-correlated genes with the two DELs are mainly enriched in the related processes of silk protein translation. This implies that these DELs may affect the phenotypic variation in silk yield between the domestic and wild silkworms through the post-transcriptional regulation of silk protein.