Dynamic transcriptome analysis of Bombyx mori embryonic development

Abstract

Bombyx mori has been extensively studied but the gene expression control of its embryonic development is unclear. In this study, we performed transcriptome profiling of six stages of B. mori embryonic development using RNA sequencing (RNA‐seq). A total of 12 894 transcripts were obtained from the embryos. Of these, 12 456 transcripts were shared among the six stages, namely, fertilized egg, blastoderm, germ‐band, organogenesis, reversal period, and youth period stages. There were 111, 48, 41, 54, 77, and 107 transcripts specifically expressed during the six stages, respectively. By analyzing weighted gene correlation networks and differently expressed genes, we found that during embryonic development, many genes related to DNA replication, transcription, protein synthesis, and epigenetic modifications were upregulated in the early embryos. Genes of cuticle proteins, chitin synthesis‐related proteins, and neuropeptides were more abundant in the late embryos. Although pathways of juvenile hormone and the ecdysteroid 20‐hydroxyecdysone, and transcription factors were expressed throughout the embryonic development stages, more regulatory pathways were highly expressed around the organogenesis stage, suggesting more gene expression for organogenesis. The results of RNA‐seq were confirmed by quantitative real‐time polymerase chain reaction of 16 genes of different pathways. Nucleic acid methylation and seven sites in histone H3 modifications were confirmed by dot blot and western blot. This study increases the understanding of the molecular mechanisms of the embryonic developmental process and information on the regulation of B. mori development.

Homeobox protein A1‐like and DNA methylation regulate embryo‐specific Zinc finger protein 615 gene expression and embryonic development in the silkworm Bombyx mori

“…The raw Illumina sequencing data from RNA‐seq conducted on embryos from 6 embryonic stages are deposited in the Sequence Read Archive with the accession number SRP292267 at the National Center for Biotechnology Information (Xu et al. , 2022a).…”

“…RNA‐seq analysis has shown that in B. mori embryos, transcription factors are expressed throughout embryonic development (Xu et al. , 2022a). Therefore, multiple pathways regulate the accurate stage‐ or tissue‐specific expression of genes to ensure proper embryonic development.…”

“…In Bombyx mori embryos, the expression levels of genes related to DNA replication, transcription, and protein translation are upregulated during the early embryonic stage, and the expression levels of genes related to cuticle proteins, chitin synthesis, and neuropeptides are upregulated during late embryonic stage, suggesting that different genes are involved in cell fate and differentiation during the early stage and organ development during the late stage (Xu et al. , 2022a). 20hydroxyecdysone‐ and juvenile hormone‐mediated hormone pathways (Makka et al.…”

“…In addition to regulators of transcription, epigenetic modifications are active during early embryonic development (Xu et al, 2022a), suggesting that epigenetic modification is involved in the regulation of embryonic development. DNA methylation, an important form of epigenetic modification, regulates early embryonic development and affects the hatching rate of insects, including B. mori (Xiang et al, 2013), Nilaparvata lugens (Zhang et al, 2015), andNasonia (Zwier et al, 2012).…”

Monitoring and modelling the dynamics of the cellular glycolysis pathway: A review and future perspectives

“…Although, the cellular genome does not change much during the lifetime of the organism, the cellular transcriptome is highly dynamic and depends on the state of the system. Several approaches for a wider range of systems at single and multi-cellular levels are already developed for dynamic transcriptome analysis [ [152] , [153] , [154] , [155] ], but by the nature of the analytical technology, these approaches are destructive and rely on quenching the systemic information at pre-fixed states.…”