The ascomycete fungus Cordyceps militaris infects lepidopteran insect pupae, forming characteristic fruiting bodies called “Dong Chung Ha Cho” in Korean. They have been used as medicines owing to their anti-allergic, anti-inflammatory, and immune-enhancing effects. This fungus can be grown on the geminated soybeans Rhynchosia nulubilis, which also contains several novel isoflavones. We performed a comparative transcriptome analysis to determine core gene sets or pathways contributing to biologically active products such as isoflavone. Initially, we sequenced 2-week-old fungal cultures on different soybean agar media, where different amounts of water agar were implemented to show different surface topology. We selected 830 upregulated and 188 downregulated genes by comparing linear models of the samples (two-fold change threshold). Gene ontology analysis identified that the “IMP biosynthesis” term was significantly found in the upregulated gene sets. The pathway is involved in the synthesis of cordycepin, the reference chemical for C. militaris. This finding in the transcriptome data is consistent with the previous observation: increased cordycepin concentrations in the C. militaris cultured on germinated soybean.

When treating the 3rd instar larvae of the diamondback moth (DBM), Plutella xylostella, with sublethal doses (LC10) of chlorantraniliprole, indoxacarb and spinosad via leaf dipping, their tolerance to insecticides was significantly enhanced. By analyzing the differentially expressed genes (DEGs), we found a number of genes that respond commonly or specifically to the test insecticides. With the criteria of p value < 0.05 and Log2FC > 1/ < -1, a total of 476, 367 and 410 genes were determined to respond specifically to chlorantraniliprole, indoxacarb and spinosad, respectively. Gene Ontology (GO) analysis revealed that the cuticle reorganization is commonly associated in all treatments and the oxidative stress-related process is also shown in all insecticides except spinosad. Finally, the DEGs seemingly related with enhanced tolerance were chosen for further characterization, and reliability of the transcriptome data were confirmed by quantitative PCR. The functional categories of these DEGs included mostly detoxification related genes, cuticle proteins, energy metabolism and transcriptional regulation. While the commonly responding DEGs suggest that they are likely involved in defense against common intoxication process, the DEGs specifically responded to each insecticide suggests the presence of unique tolerance mechanisms to each insecticide depending on their different structure and mode of action. Their possible roles in the tolerance/resistance development were discussed.

Drosophila melanogaster is mainly found in fermented and rotten fruits and is tolerant to chemicals emitted during the fermentation process. Its distinctive habitat suggests an evolutionary adaptation to environmental chemicals. In order to understand the physiological adaptation of D. melanogaster to the chemicals, we treated LC20 concentration of three chemicals (acetic acid, ethanol and 2-phenylethanol) and differential expression of the female whole body transcripts were compared with control fly (no chemical treatment). Compared to control fly, 94, 137 and 59 genes were up-regulated, while 85, 184 and 166 genes were down-regulated in acetic acid, 2-phenylethanol and ethanol treated flies, respectively. According to the KEGG enrichment analysis, genes categorized in metabolic pathway, Toll/IMD signaling pathway, lysosome and autophagy were ranked in the top groups of most changed gene sets after three chemical treatment. In addition, we selected 7 genes showing different expression levels in transcriptome analysis, and investigated their expression changes in the flies exposed to various concentration of three chemicals using quantitative PCR.

Bemisia tabaci is a species complex consist of about 40 cryptic species. This species is also a vector of at least 100 begomovirus including Tomato yellow leaf curl virus (TYLCV). TYLCV transmitted by B. tabaci in a circulative propagative manner but its molecular mechanism is remain unclear. We investigate the transcriptional response of B. tabaci MED to TYLCV infection using next generation sequencing (NGS) analysis. In total 16757 differentially expressed genes between viruliferous and non-viruliferous whiteflies were analyzed. Among them 289 transcripts found significant, where 116 up-regulated and 173 down-regulated. Our results reveal the whitefly-TYLCV relationship and provide important molecular information about virus transmission of vector insects.

Korean Native Pig (KNP) has a uniform black coat color, excellent meat quality, white colored fat, solid fat structure and good marbling. However, its growth performance is low, while the western origin Yorkshire pig has high growth performance. To take advantage of the unique performance of the two pig breeds, we raised crossbreeds (KNP × Yorkshire to make use of the heterotic effect. We then analyzed the liver transcriptome as it plays an important role in fat metabolism. We sampled at two stages: 10 weeks and at 26 weeks. The stages were chosen to correspond to the change in feeding system. A total of 16 pigs (8 from each stage) were sampled and RNA sequencing was performed. The reads were mapped to the reference genome and differential expression analysis was performed with edgeR package. A total of 324 genes were found to be significantly differentially expressed (|log2FC| > 1 & q < 0.01), out of which 180 genes were up-regulated and 144 genes were down-regulated. Principal Component Analysis (PCA) showed that the samples clustered according to stages. Functional annotation of significant DEGs (differentially expressed genes) showed that GO terms such as DNA replication, cell division, protein phosphorylation, regulation of signal transduction by p53 class mediator, ribosome, focal adhesion, DNA helicase activity, protein kinase activity etc. were enriched. KEGG pathway analysis showed that the DEGs functioned in cell cycle, Ras signaling pathway, p53 signaling pathway, MAPK signaling pathway etc. Twenty-nine transcripts were also part of the DEGs, these were predominantly Cys2His2-like fold group (C2H2) family of zinc fingers. A protein-protein interaction (PPI) network analysis showed that there were three highly interconnected clusters, suggesting an enrichment of genes with similar biological function. This study presents the first report of liver tissue specific gene regulation in a cross-bred Korean pig.