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.

멸종위기종의 복원에 있어 복원대상종의 도입 후 유전적 모니터링과 관리에 있어 핵심은 유전적으로 건강한 개체군을 유지하는 것이다. 한국에서 멸종위기야생생물 I급인 여우의 복원사업이 진행되어 오면서 복원을 위해 5년 간 유전적으로 동일한 계통에 속하는 여우들이 원종으로써 동북아 시아 지역에서 도입되어져 왔으나, 도입종들의 유전적인 건강성 확인은 그 평가가 이루어지지 않고 있는 실정이다. 본 연구는 도입 여우 11개체에 대한 유전적 다양성 확보 여부와 개체 간 유전적 차이를 확인하고자 수행되었다. 대상 개체들의 유전적 다양성은 샘플의 RNA sequencing 결과로부터 SNP을 확인하는 방법으로 분석하였다. 현재 한국산 여 우(Vulpes vulpes)와 관련한 전체 유전체의 정보는 전무한 실정이며, 적절한 참조 데이터 세트의 부재로는 SNP의 비교와 그 다양성 수준을 결정할 수 없기 때문에, 본 연구에서는 분석 대상 개체를 포함한 전체 샘플의 RNA-seq data를 transcriptome DB로 제작하여 reference로 활용하였다. 이 reference data를 사용하여 SNP을 탐색하고 유전적 다양성 정도(π)를 계산한 결과. π는 평균 2.287*10-4bp-1의 낮은 값을 나타내었으며, 본 결과로 여러 멸종위기 야생 동물들의 기존 π값들과 비교하고, 각 개체 간 산점도의 표현을 통해 유전적다양성의 상대적인 수준과 그 위치를 확인하였다. 본 연구 결과는 복원정책 수립에 있어 추가 도입되는 여우의 선정 기준의 바탕이 되는 자료 등으로 활용 될 수 있을 것으로 판단된다.

The red imported fire ant (Solenopsis invicta) is a species of ant native to South America. The fire ant was inadvertently introduced into USA, Australia, New Zealand, and other Asian countries including China and Taiwan. Since the first report of the fire ant in port city of Busan, Korea in 2017, it was found in many other cities of Korea in following year. To obtain the molecular information of this invasive species, total RNA was extracted from the abdominal segment of the ants collected in Incheon, and subjected to transcriptome sequencing. By using Illumina sequencer platform, 101 base pared-end sequencing generated 2 × 50,064,081 of raw reads to obtain 2 × 45.95 Gbase of quality filtered nucleotide sequences. The in silico cDNA library was constructed by Trinity de novo assembler followed by TransDecoder ORF finder and CD-HIT clustering program to streamline the library. The final version of cDNA library contains 20,442 contigs with protein coding capability. To survey the virome of this ant, these contigs were searched against the viral reference sequences from NCBI RefSeq database with BLASTN program. As a result, contigs which showed high sequence identities with several RNA viruses including previously reported SINV-2 were found from the fire ant. This virome information might give an idea of a shift of virological environment of this newly found ant isolate or population in Korea.

Laodelphax striatellus is an important pest of rice due to not only sucking rice seedlings, but also transmitting serious plant viruses. Among various kinds of insecticide groups (carbamates, organophosphorus, neonicotinoids, etc.), carbofuran, a systemic carbamate insecticide, has been most extensively used to control rice pests including L. striatellus, resulting in widespread carbamate resistance in Korea and other Northeast Asia countries. To identify the genes associated with carbofuran resistance, we obtained a 14-fold higher resistant strain (SEL9) from the mixed-field population (SEL0) by consecutive selection. A transcriptome-based analysis was conducted and differentially expressed genes (DEG) were compared between the SEL9 and SEL0 strains. A total of 96,185,150 reads were analyzed, of which 62,860,430 reads were mapped. From these reads, 15,356 transcripts were annotated. A total of 327 up-regulated and 275 down-regulated genes were identified in the resistant SEL9 strain compared to SEL0 strain by DEG analysis. Gene ontology (GO) analysis was performed using DEGs showing statistical significance (P < 0.05). The GO analysis identified 1,320 genes in biological process group, 1,100 genes in cellular component group and 428 genes in molecular_function group.

The varroa mite, Varroa destructor, is a small ectoparasitic mite which attacks honeybee, Apis mellifera, and also known to harbor small RNA viruses which infect honeybees. To survey the transcriptome of varroa mite, total RNA of female adult mites was subjected to RNA-seq to construct an in silico cDNA library. 2 × 8.3 Gbase of quality filtered paired-end nucleotide sequences were obtained to construct 28,302 of protein-coding contigs by de novo assembly, and subsequent BLAST search revealed the viruses infect honeybee or associated with varroa mites. Six of the contigs showed high sequence identity to Iflavirus, picorna-like virus, rhabdovirus, and macula-like virus were discovered. It implies that the viral flora in varroa mites and honeybees might be more complex than previously studied, and suggests the importance of further virome studies for better understanding of honeybee health.

The bean bug is one of major hemipteran pests against the soybean, Glycine max in Korea. Gene expression regulation technologies such as RNA interference and gene editing have emerged as a next generation pest control strategy in agriculture. To search genes effective to feeding inhibition with exogenous dsRNA, a total of 26,761 transcripts were obtained from salivary glands of the bean bug and several target gene candidates such as GPCR, OBP, and CSP were profiled in this study. On the other hand, 1st instar nymphs of the bean bug after hatching were highly attracted to water and absorbed about 701.5 ± 137.72 ㎍/individual/day, suggesting that it could be a practical way for RNA interference by feeding exogenous dsRNA dissolved in water. These preliminary results are expected to be helpful to investigate novel pest control strategy of R. pedestris in the future.