Ticks and mosquitoes are well known as the most dangerous animals in the world. During the blood feeding, they can transmit a variety of pathogens (bacteria, virus, and protozoa) causing human diseases such as SFTS (severe fever with thrombocytopenia syndrome), malaria, Zika, and dengue. In Korea, SFTS is a newly emerging vector-borne disease transmitted by Asian longhorned tick, Haemaphysalis longicornis. However, there are no effective methods to control ticks and tick-borne disease. The laboratory of medical entomology at Kyungpook national university is focusing on not only fundamental biology of hard ticks in Korea including life cycle and host ranges but molecular physiology and comparative transcriptomics to understand interactions between vector and pathogen at the molecular level. We are also focusing on molecular physiological mechanisms of mosquito salivary secretion by investigating the function of neuropeptides and G protein-coupled receptors (GPCRs) in the salivary glands of Asian tiger mosquito, Aedes albopictus. We believe that understanding the biology of blood feeding arthropods will lead us to the development of novel methods for the disruption of feeding, thus allowing for the prevention of pathogen transmission.

Insect cuticle tanning (pigmentation and sclerotization) is a complex and vital physiological process that begins with tyrosine and is responsible for production of both melanin- and quinoid-type pigments. In addition, these quinones undergo isomerization to quinone methides and cross-linking reactions with cuticular proteins for cuticle sclerotization. In this study, we studied the functions of TmDDC and TmY-y as well as TmNAT1, TmADC and Tmebony from Tenebrio molitor, which are involved in the tyrosine-derived melanin- and quinoid-type pigment productions, respectively. The temporal and spatial expression patterns of the genes were analyzed by real-time PCR. RNA interference was performed to understand the genetic regulation and molecular mechanism underlying the darkening and hardening of beetle cuticle.

Insect structural cuticular proteins (CPs) play a major role in determining the diverse physical properties of the cuticle as a result of interactions/cross-linking among themselves and with chitin. CP genes compose a large gene family and have been classified more than ten distinct families based on the presence of unique amino acid sequence motifs. In this study, we performed RNAi-based functional analysis of eleven genes (TcCPLCP1-11) in Tribolium castaneum, which belong to CPLCP (Cuticular Proteins of Low Complexity, Proline rich) cuticular protein family. RNAi for TcCPLCP7-11 caused lethal pupal-adult molting defects and/or abnormal cuticle morphology in the resulting adults. Ultrastructural defects of the cuticles from TcCPLCP7-11-deficient insects by TEM are also discussed.

Insects have a protective exoskeleton consisted with cuticle to adapt various environments and pathogens. Insect cuticle mainly composed of the polysaccharide chitin and numerous of cuticular proteins (CPs). CPs are important for insect cuticle formation, development, and growth because it produces proper combination of mechanical and physical properties of cuticle depend on the regions of an exoskeleton. The largest family of CPs contains a 28-residue motif known as the Rebers-Riddiford (R&R) consensus sequence. When sequences containing the R&R consensus are aligned, they fall into three groups based on sequence similarity, and these groups tend to correlate with the type of cuticle (soft or hard) from which the proteins are derived. Proteins with the RR-1 motif have been found primarily in soft cuticle, whereas many proteins from rigid cuticle have an extended region of similarity called RR-2. We recently reportedthat two major CPs, TcCPR18 and TcCPR27 belong to RR-2, are essential for formation of highly sclerotized modified-forewings (elytra) of a beetle. In this study, we performed functional genomics of TcCPR4, which encodes RR-1 motif. The transcript levels of TcCPR4 drastically increased in 3 d-old pupae at when adult cuticle synthesis appears to be begun. Immunohistochemical studies revealed that TcCPR4 protein was detected in the rigid cuticle of elyton and ventral abdomen but not in the flexible cuticle of hindwing and dorsal abdomen of T. castaneum adult. Furthermore, TcCPR4 protein was specifically present at basal side of the procuticle (near the epidermal cells) and vertical canals, whereas TcCPR27 protein was found entire procuticle. Injection of double-stranded RNA of TcCPR4 (dsTcCPR4) into late instar larvae had no effect on development and any types of molting such as larval-larval, larval-pupal or pupal-adult. Interestingly, depletion of both TcCPR4 and TcCPR27 transcripts could rescue the elytral cuticle defect and mortality produced by injection of dsTcCPR27 alone. Transmission electron microscopy analysis revealed that depletion of TcCPR4 had abnormal vertical canals in rigid adult cuticle while dsTcCPR27 injection showed less electron-dense-horizontal laminae and vertical canals. Surprisingly, co-injection of dsRNA for TcCPR4 and TcCPR27 exhibited more severe cuticle defect with thinner elytral cuticle and abnormal vertical canals and chtin laminae compared to those from insects treated with dsRNA for each gene. These results suggest that TcCPR4 as a RR-1 is essential structural component in the rigid cuticle of T. castaneum adult.

Although decapod crustaceans are one of the most important fisheries resources with high market value, we still have only limited knowledge about their basic physiology related to growth, development, and reproduction. This is mainly due to the lack of tools to manipulate genetic information leading the phenotype changes. Recently physiological study for decapod crustaceans changed dramatically by both the development of next-generation sequencing (NGS) technology and RNA interference (RNAi). Significant decrease in the cost for reading genome or transcriptome allowed the even single lab can manage the omics-level study about the non-model system, decapod crustaceans. As genomic and transcriptomic data increased, we are able to screen novel genes in decapod crustaceans related to growth and development. As another useful tool, gene silencing through RNAi is gaining momentum for decapod crustaceans. RNAi has proven instrumental in a growing number of crustacean species, revealing the functionality of novel crustacean genes. Major research topics in decapod crustaceans include immune response, reproduction, development, homeostasis, molting and growth, and environmental stress. In addition to any changes in phenotype, tanscriptomic analysis induced by the specific gene knockdown by RNAi extended our knowledge of physiological responses of novel crustacean genes. Those new techniques extend our knowledge about crustacean physiology providing the basis for increasing productivity of decapod crustaceans.

In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for screening target loci with agricultural traits. We propose the variation block method, a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing short-read DNA sequences of the cultivar to a reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are named as variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybeans and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. We suggest that the variation block method is an efficient genomics method for recombination block-level comparison of crop genomes. We expect that this method holds the prospect of developing crop genomics by bringing genomics technology to the field of crop breeding.

Although much effort has been made to find agronomically important loci in the soybean plant, extensive linkage disequilibrium and genome duplication have limited efficient genome-wide linkage analyses that can identify important regulatory genes. In this respect, recombination block-based analysis of cultivated plant genomes is a potential critical step for molecular breeding and target locus screening. We propose a new three-step method of detecting recombination blocks and comparative genomics of bred cultivars. It utilizes typical reshuffling features of their genomes, which have been generated by the recombination processes of breeding ancestral genomes. To begin with, mutations were detected by comparing genomes to a reference genome. Next, sequence blocks were examined for likenesses and difference with respect to the reference genome. The boundaries between the blocks were taken as recombination sites. All recombination sites found in the cultivar set were used to split the genomes, and the resulting sequence fragments were named as core recombination blocks (CRBs). Finally, the genomes were compared at the CRB level, instead of at the sequence level. In the genomes of the five Korean soybean cultivars used, the CRB-based comparative genomics method produced long and distinct CRBs that are as large as 22.9 Mb. We also demonstrated efficiency in detecting functionally useful target loci by using indel markers, each of which represents a CRB. We further showed that the CRB method is generally applicable to both monocot and dicot crops, by analyzing publicly available genomes of 31 soybeans and 23 rice accessions.

The plant cell wall is an extracellular matrix, which can be viewed as a multifunctional subcellular compartment involving many fields of research: growth and development, plant-pathogen interactions, stress, cell-to-cell signaling, metabolic processes, biomaterials and biofuels, and many others. Given its importance, much of the research effort has been directed toward investigating the plant cell walls containing plant cell wall proteins, which are essential constituents of plant cell walls and play essential roles in many biological processes, and yet there is still not a distinct repertoire of the plant cell wall proteins. Several functional screen procedures including a yeast secretion trap, an Agrobacterium-mediated transient expression assay and a subcellular localization study, have been recently optimised to confirm secretion and localization of an ever-growing list of plant cell wall proteins. These functional screen approaches collectively provide a powerful suite of means to identify and characterize a dynamic and complex plant cell wall proteome. Thus, the potential outcomes of plant cell wall functional genomics will enable plant breeding programs to develop new strategies for improvement of crop quality.

TILLING (Targeting Induced Local Lesions IN Genomes) is broadly regarded as an excellent methodology for reverse genetics applications. Approximately 15,000 M3 TILLING lines have been developed via the application of gamma-ray irradiation to rice seeds (cv. Donganbyeo), followed by subsequent selections. In an effort to evaluate the genetic diversity of the TILLING population, we have employed the AFLP multiple dominant marker technique. A total of 96 (0.64%) TILLING lines as well as Donganbyeo were selected randomly and their genetic diversity was assessed based on AFLP marker polymorphisms using 5 primer combinations. An average of 100.4 loci in a range of 97 to 106 was detected using these primer combinations, yielding a total of 158 (31.4%) polymorphic loci between Donganbyeo and each of the 96 lines. A broad range of similarity from 80% to 96% with an average of 89.4% between Donganbyeo and each of the 96 lines was also observed, reflecting the genetic diversity of the TILLING population. Approximately 28 polymorphic loci have been cloned and their sequences were BLAST-searched against rice whole genome sequences, resulting in 20 matches to each of the gene bodies including exon, intron, 1 kb upstream and 1 kb downstream regions. Six polymorphic loci evidenced changes in the coding regions of genes as compared to the rice pseudomolecules, 4 loci of which exhibited missense mutations and 2 loci of which exhibited silent mutations. Therefore, the results of our study show that the TILLING rice population should prove to be a useful genetic material pool for functional genomics as well as mutation breeding applications.

High level of sequence similarity and genetic conservation within plants of same family allow us to use the informations and cDNA microarray obtained from a model plant such as Arabidopsis for better understanding of non-model plants within the same family, for example, rapeseed. Several lines of rapeseed plants with different sensitivity to cold stress were selected and the gene expression profiles under cold stress were examined using 1.6K specialized cDNA microarray. For the comparative analysis between Arabidopsis, economic plants and rapeseed, we adopted a recently developed computational method called "Gene Set Enrichment Analysis (GSEA)" which determines whether defined set of genes show statically significant and concordant differences between two biological states. Along this, five different gene sets including a network gene set based on a regulatory gene network model for early cold stress response and a co-expression gene set based on ∼ 1,500 expression data were built in this lab. With these gene sets and GSEA method, the expression data was analyzed to pinpoint the group of genes potentially responsible for the difference of stress sensitivity between two different plants. Since the plant encounters stress combinations concurrently or separated temporally and must present an integrated response to them, we built 'Cross-talk map' using ∼ 63 expression data of Arabidopsis under 9 different environmental stresses. Utilizing this cross-talk map, the significance of the identified group of genes was evaluated for their practical application to enhance stress tolerance. Currently, we identified several promising genes at a cross-talk point and are pursuing transgenic engineering to enhance the stress tolerance against more than two stress conditions.