Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms (Bombyx mori)

SIMPLE SUMMARY: The sericulture industry in the Philippines remains to be enhanced through efforts to improve local strains of the silkworm Bombyx mori, such as selective hybridization. Genetic trait markers could help improve breeding; however, there is a scarcity of genetic data on local strains. This study aims to bridge this gap by analyzing the gene expression profiles of Philippine-reared silkworm strains through next-generation sequencing. Transcriptome assemblies were generated, and gene expressions were compared between silkworm strains reared in different temperatures, revealing genes that may be important for development in a tropical environment. This study is the first to provide transcriptome datasets for the Philippine-reared B. mori strains, which may serve as a resource for improving local strains and increasing silk production. ABSTRACT: RNA sequencing was used to assemble transcriptome data for Philippine-reared silkworm and compare gene expression profiles of strains reared in high- and low-temperature environments. RNA was isolated from the silk glands of fifth instar larvae and mRNA-enriched libraries were sequenced using Illumina NextSeq 500. Transcriptome reads were assembled using reference-based and de novo assemblers, and assemblies were evaluated using different metrics for transcriptome quality, including the read mapping rate, E90N50, RSEM-eval, and the presence of single-copy orthologs. All transcriptome assemblies were able to reconstruct >40,000 transcripts. Differential expression analysis found 476 differentially expressed genes (DEGs; 222 upregulated, 254 downregulated) in strains reared in different temperatures. Among the top DEGs were myrosinase, heat shock proteins, serine protease inhibitors, dehydrogenases, and regulators of the juvenile hormone. Validation of some of the top DEGs using qPCR supported the findings of the in silico analysis. GO term enrichment analysis reveals an overrepresentation of GO terms related to nucleotide metabolism and biosynthesis, lipid and carbohydrate metabolic processes, regulation of transcription, nucleotide binding, protein binding, metal binding, catalytic activity, oxidoreductase activity, and hydrolase activity. The data provided here will serve as a resource for improving local strains and increasing silk production of Philippine-reared B. mori strains.