Construction of a simple evaluation system for the intestinal absorption of an orally administered medicine using Bombyx mori larvae

Systematic identification of smORFs in domestic silkworm (Bombyx mori)

The silkworm (Bombyx mori) is not only an excellent model species, but also an important agricultural economic insect. Taking it as the research object, its advantages of low maintenance cost and no biohazard risks are considered. Small open reading frames (smORFs) are an important class of genomic elements that can produce bioactive peptides. However, the smORFs in silkworm had been poorly identified and studied. To further study the smORFs in silkworm, systematic genome-wide identification is essential. Here, we identified and analyzed smORFs in the silkworm using comprehensive methods. Our results showed that at least 738 highly reliable smORFs were found in B. mori and that 34,401 possible smORFs were partially supported. We also identified some differentially expressed and tissue-specific-expressed smORFs, which may be closely related to the characteristics and functions of the tissues. This article provides a basis for subsequent research on smORFs in silkworm, and also hopes to provide a reference point for future research methods for smORFs in other species.

Co-Expression Network and Time-Course Expression Analyses to Identify Silk Protein Regulatory Factors in Bombyx mori

Simple Summary

Previous studies have reported how the silk production ability of Bombyx mori can be enhanced, but the mechanism that regulates silk protein genes remains unclear. We performed co-expression network analysis using networkz, an in-house program, which led to the identification of 91 transcription factors were co-expressed with silk protein genes. Of them, 13 transcripts were identified to be novel regulatory factors by time-course expression analysis during the fifth instar larvae stage. Their expression patterns were highly relevant to those of silk protein genes. Our results suggest that the two-step expression screening was robust and highly sensitive to screen relative genes, and a complex mechanism regulates silk protein production in B. mori. The novel candidates that were identified herein can serve as key genes to develop methods to enhance the silk protein production ability of B. mori.

Abstract

Bombyx mori is an important economic insect and an animal model in pharmacomedical research. Although its physiology has been studied for many years, the mechanism via which silk protein genes are regulated remains unclear. In this study, we performed two-step expression screening, namely co-expression network and time-course expression analyses to screen silk protein regulation factors. A co-expression network analysis using RNA-seq data that were obtained from various tissues, including the silk glands of B. mori, was performed to identify novel silk protein regulatory factors. Overall, 91 transcription factors, including some known ones, were found to be co-expressed with silk protein genes. Furthermore, time-course expression analysis during the fifth instar larvae stage revealed that the expression pattern of 13 novel transcription factors was highly relevant to that of silk protein genes and their known regulatory factor genes. In particular, the expression peak of several transcription factors (TFs) was detected before the expression of silk protein genes peak. These results indicated that a larger number of genes than expected may be involved in silk protein regulation in B. mori. Functional analyses of function-unknown transcription factors should enhance our understanding of this system.

Reference Transcriptome Data in Silkworm Bombyx mori

Herein, we performed RNA-seq analysis of ten major tissues/subparts of silkworm larvae. The sequences were mapped onto the reference genome assembly and the reference transcriptome data were successfully constructed. The reference data provided a nearly complete sequence for sericin-1, a major silk gene with a complex structure. We also markedly improved the gene model for other genes. The transcriptomic expression was investigated in each tissue and a number of transcripts were identified that were exclusively expressed in tissues such as the testis. Transcripts strongly expressed in the midgut formed tight genomic clusters, suggesting that they originated from tandem gene duplication. Transcriptional factor genes expressed in specific tissues or the silk gland subparts were also identified. We successfully constructed reference transcriptome data in the silkworm and found that a number of transcripts showed unique expression profiles. These results will facilitate basic studies on the silkworm and accelerate its applications, which will contribute to further advances in lepidopteran and entomological research as well as the practical use of these insects.