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Differentially expressed genes (DEGs) in oviducts of Yun7 and its giant egg mutant Yun7Ge of silkworm, Bombyx mori

ABSTRACT: Yun7Ge (Yun7Ge is represented by Ge in the high-throughput sequencing results) is a giant egg mutant found in the silkworm variety Yun7 (Yun7 is represented by Se in the high-throughput sequencing results). The amount of laid eggs and the hatching rate of Yun7Ge are reduced, which is not conducive to the reproduction. The target gene controlling giant egg trait is located on the Z chromosome (chromosome 1) was determined through genetic analysis. To find mutant gene and explore the relationship between mutant gene and giant egg trait, the differentially expressed genes (DEGs) in the oviducts of Yun7 and Yun7Ge were analyzed by high-throughput sequencing, and two replicates were set for each sample. ∣log 2∣>1, the value of FPKM>100 and the genes were up-regulated or down-regulated in giant eggs of the two replicates as the standard for screening DEGs. A total of 65 DEGs were screened. Among these DEGs, 7 genes were up-regulated and 58 genes were down-regulated in giant eggs. These DEGs were classified according to the chromosome where the genes are located. The results showed that there was only one DEG (PHYHD1) on chromosome Z, and it was almost not expressed in giant eggs. Interestingly, there were 35 DEGs on chromosome 2, including 25 chorion genes, and these 25 genes are all down-regulated. After knocking out the PHYHD1 using CRISPR/Cas9, the chorion genes were significantly down-regulated. These results indicate that the silencing of PHYHD1 leads to the down-regulation of many chorion protein genes, which may be the direct cause of giant eggs.

ORGANISM(S): Bombyx mori

PROVIDER: GSE173672 | GEO | 2021/05/01

REPOSITORIES: GEO

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Project description:Over the past decades, Helicoverpa armigera nucleopolyhedrovirus (HearNPV) has been widely used for biocontrol of cotton bollworm, which is one of the most destructive pest insects in agriculture worldwide. However, the molecular mechanism underlying the interaction between HearNPV and host insects remains poorly understood. In this study, high throughput RNA-sequencing was integrated with label-free quantitative proteomics analysis to examine the dynamics of gene expression in the fat body of H. armigera larvae in response to challenge with HearNPV. RNA-sequencing-based transcriptomic analysis indicated that host gene expression was substantially altered, yielding 3,850 differentially expressed genes (DEGs), while no global transcriptional shut-off effects were observed in the fat body. Among the DEGs, 60 immunity-related genes were down-regulated after baculovirus infection, a finding that was consistent with the results of quantitative real-time RT-PCR (qRT-PCR). Gene ontology and functional classification demonstrated that the majority of down-regulated genes were enriched in gene cohorts involved in energy, carbohydrate, and amino acid metabolic pathways. Proteomics analysis identified differentially expressed proteins in the fat body, among which 76 were up-regulated, whereas 373 were significantly down-regulated upon infection. The down-regulated proteins are involved in metabolic pathways such as energy metabolism, carbohydrate metabolism (CM), and amino acid metabolism, in agreement with the RNA-seq data. Furthermore, correlation analysis suggested a strong association between the mRNA level and protein abundance in the H. armigera fat body. More importantly, the predicted gene interaction network indicated that a large subset of metabolic networks was significantly negatively regulated by viral infection, including CM-related enzymes such as aldolase, enolase, malate dehydrogenase and triose-phosphate isomerase. Taken together, transcriptomic combined with proteomic data elucidated that baculovirus established systemic infection of host larvae, and manipulated the host mainly by suppressing the host immune response and down-regulating metabolism to allow viral self-replication and proliferation. Therefore, this study provided important insights into the mechanism of host-baculovirus interaction.

Project description:Purpose: To elucidated key metabolic pathways important for S. Enteritidis survival in egg white. Methods: RNA sample of Mid-log phase bacteria cultures that grown in M9FeS medium were taken as 0h sample, and bacteria incubated with egg white for 6h 12h and 24h were taken as 6,12,24h RNA sample respectively. Three biological replicates were carried out per sample. RNA sample was sequenced with Illumina HiSeq 2000 System. DESeq2 method was used to calculate the differentially expressed genes. qRT–PCR and gene mutation were used to validate RNA-seq result. Results: A total of 12 samples were sequenced. The average output of each sample was 1.33 Gb, and the average comparison rate with the reference genome was 97.51%. M9FeS and egg whites cultivation resulted in 2400 to 2700 expressed genes accounting for 53 to 58% of the whole genome. In this group, 1240 to 1470 genes had significant levels of log2 fold changes ≥1, (Padj <0.05) compared with control. These accounted for 27.3 to 32.2% of the whole genome indicating a large shift in the transcriptional response to egg whites. qRT–PCR result of 21 selected genes highly consistent with the RNAseq results at all three timepoints. 8 out of 12 DEGs mutants showed decreased survival ability in egg white, suggested that the DEGs from the RNAseq results correlated significantly with the egg white resistance phenotype. Conclusions: Using strand-specific RNA sequencing, we found pathways significantly changed in egg white. Genes involved in SOS-dependent and independent DNA damage repair, alkaline pH adaption, osmotic stress adaption, envelope damage repair including maintaining periplasm homeostasis and reinforcing peptidoglycan layer, nitrogen assimilation, Salmonella pathogenicity island 2, iron absorption and biotin synthesis, were significantly up regulated in bacteria surviving in egg whites. Differentially expressed genes involved in energy metabolism, translation, and cell motility, Salmonella pathogenicity island 1 were significantly down-regulated in egg whites.

Dataset Information

Differentially expressed genes (DEGs) in oviducts of Yun7 and its giant egg mutant Yun7Ge of silkworm, Bombyx mori

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