Spodoptera eridania and S. ornithogalli (Lepidoptera: Noctuidae), which are polyphagous pests that damage various crops such as tomatoes and beans are regulated quarantine species that are highly likely to invade South Korea. Therefore, it is crucial to promptly and accurately identify the presence of S. eridania and S. ornithogalli in crop fields to effectively eradicate as a regulated quarantine species. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay, which allows for rapid in-field identification. To develop the LAMP　assay, we selected target species-specific genomic regions from the whole-genome sequences of one target and 13 other lepidopteran species. We validated each five and six primer sets that consistently produced positive reactions in S. eridania and S. ornithogalli, respectively. To test the sensitivity of the each locus, LAMP reactions were performed using various reaction times using crude DNA, which was extracted from various types of adult tissues. All sensitivity tests were also successful.

Bacillus velezensis TJS119 was isolated from the freshwater, and antagonistic activity against of pathogenic fungi. Strain TJS119 showed a broad spectrum of antagonistic activities many fungal pathogens, including the green muscardine fungus Metarhizium anisopliae. The whole-genome sequence of B. velzensis TJS119 was analyzed using the illumina platform. The genome comprises a 3,809,913 bp chromosome with a G + C content of 46.43%, 3,834 total genes, 10 rRNA and 73 tRNA genes. The genome contained a total of 8 candidate gene clusters (difficidin, fengycin, bacillaene, macrolactin, bacillibactin, bacilysin, surfactin and butirosin) to synthesize secondary metabolite biosynthesis. Overall, our data will aid future studies of the biocontrol mechanisms of B. velezensis TJS119 and promote its application in insect disease control.

국내 유입 가능성이 높은 검역 관리해충인 Spodoptera eridania 및 S. ornithogalli는 전 세계적으로 토마토, 콩 등 여러 종의 작물을 가해하는 광식성 해충이다. 이에 따라 국내 유입 시 해당 작물에 높은 경제적 피해를 입힐 가능성 이 있으므로 신속 정확한 진단이 필요한 실정이다. 따라서 본 연구에서는 상기 두 종을 대상으로 현장 활용이 가능한 LAMP 진단법 개발을 수행하였다. 표적종 두 종 및 비표적종 11종(국내 발생 Spodoptera 종 및 동일 기주 가해종 등)의 전장유전체 정보를 확보한 후 비교 분석을 통해 각 표적종 별 특이적 영역을 확보한 후 해당 영역을 대상으로 LAMP 프라이머를 제작하였다. DNA 농도 10 ng/μL, 반응시간 40분을 기준으로 LAMP 진단을 수행한 결과, Spodoptera eridania는 5개의 LAMP 진단 마커를 개발하였고, S. ornithogalli는 3개의 LAMP 진단 마커를 개발하였다.

고추는 한국에서 매우 중요한 양념 중 하나이다. 하지만 수입 고춧가루와 다진 양념(다대기)에 부과되는 관세율(45%/270%)의 차이로 인해, 다진 양념이 수입된 후, 건 조 및 분쇄 과정을 거쳐 고춧가루로 제작되고 있는 실정 이다. 본 연구에서는 종 특이 PCR 기술과 whole-genome amplification 방법을 접목하여 고춧가루(N=45) 및 다진 양 념(N=5) 제품의 사용원료(고추, 마늘, 양파, 파, 생강)를 분 석하였다. 모니터링 결과, 39개 고춧가루 제품은 표시사항 을 준수하였으며, 6개 고춧가루 및 5개 다진 양념 제품은 제조 기준을 충족시키지 못했다. 따라서 분석 제품의 22% 가 표시사항을 준수하지 못한 것으로 밝혀졌으며, 본 연구에 사용한 분석 방법은 고춧가루 제품에 사용된 원료 분석에 적합한 방법임을 입증하였다.

Alterations affecting the status of robustness and health can bring about physiological changes including hematological parameters in pigs. To identify quantitative trait loci (QTL) associated with 8 hematological phenotypes (one leukocyte trait, six erythrocyte traits, and one platelet trait), we performed a genome-wide association study using the Porcine SNP 60K BeadChip in an intercross population between Landrace and Korean native pigs. A total of 36,740 SNPs from 816 F2 offspring were analysed for each blood related traits after filtering by quality control. Data were analysed genome-wide rapid association using the mixed model and regression (GRAMMAR) approach. A total of 257 significant SNPs (P<1.36x10-6) on SSC3, 6, 8, 13, and 17 were detected for blood related traits in this study. Interestingly, the genomic region between 17.9 and 130 Mb on SSC8 was found to be significantly associated with RBC, MCV, and MCH. Our results include 5 significant SNPs within five candidate genes (KIT, IL15, TXK, ARAP2, and ERG) for hematopoiesis. Further validation of these identified SNPs could give valuable information for understanding the variation of hematological traits in swine.

Recently, we published a microinjection method for generating transgenic cattle using the DNA transposon system and their analysis by next-generation sequencing (Yum et al. Sci Rep. 2016 Jun 21;6:27185). In that study, we generated transgenic cattle using two different types of DNA transposon system, sleeping beauty (SB) and piggybac (PB), carrying Yellow fluorescent protein with SB (SB-YFP, female) and green fluorescent protein with PB (PB-GFP, male) under the control of the ubiquitous CAG promoter, respectively. The female and male founder cattle have been grown up to date (the female age: 40 months old, the male age: 33 months old) without any health issues. In genomic instability and blood analysis, there was no significant differences between wild type and founder cattle. In the present study, we confirmed germ-line transmission of the transposon-mediated transgene integrations and ubiquitous and persistent expression of transgene in second generation of offspring (F1). The F1 was born without any assistance and expressed GFP in the eyes without UV light. The ubiquitous expression of GFP was detected in skin fibroblast from the ear tissue and confirmed by genomic DNA PCR, which suggest that the transgene from the PB-GFP was successfully transmitted. Unfortunately, no transgene from SB-YFP were identified. To confirm the transgene integration site, the genomic DNA from blood was extracted and performed next-generation sequencing (NGS). The GFP gene was integrated in chromosome 4 (two copies), and 6. As results, a total of two copies of paternal transgene transmitted into the F1. All the integrated position was not related with coding region and there was no significant difference in genomic variants between transgenic and non-transgenic cattle. To our knowledge, this is the first report of germ-line transmission through non-viral transgenic founder cattle. Those transgenic cattle will be valuable resource to many fields of biomedical research and agricultural science.

Lentinula edodes, the popular shiitake mushroom, is one of the most important cultivated edible mushrooms. It is used as a food and for medicinal purposes. Here, we present the 46.1 Mb draft genome of L. edodes, comprising 13,028 predicted gene models. The genome assembly consists of 31 scaffolds. Gene annotation provides key information about various signaling pathways and secondary metabolites. This genomic information should help establish the molecular genetic markers for MAS/MAB and increase our understanding of the genome structure and function.

Rice stripe virus (RSV) is one of the serious plant pathogenic viruses for rice and mediated by small brown planthopper, Laodalphax striatellus. So far, the studies have been mainly focused on the interaction between the host plant and the virus. In this study, for better comprehension of the interactions among Rice stripe virus, rice and small brown planthopper, transcriptomes of the RSV-viruliferous (RVLS) and non-viruliferous L. striatellus (NVLS) were comparatively analysed. For this, non-viruliferous L. striatellus were collected from non-infected rice field and fed RSV-infected rice for 5 days. With the RNAs prepared from the RSV-viruliferous and the non-viruliferous small brown planthoppers, we conducted Illumina RNA sequencing (Hiseq 2000) and then two transcriptome databases were generated from RVLS and NVLS, respectively. The transcriptome of RVLS and NVLS were campared to figure out how the gene expression of the insects affected by Rice Stripe Virus. RSV-dependently regulated genes analysed from this study may have important functions in the transmission and replication of RSV.

Previously, we demonstrated the presence of a second copy of LPS myristoyl transferase in enterohemorrhagic Escherichia coli O157:H7, an important zoonotic diarrheagenic food-borne pathogen; the pO157-encoded ecf (an eae-conserved fragment) and the chromosomally-encoded lpxM (also referred to as msbM) genes. Although both genes share the same function as an LPS myristoyl transferase, the pO157-encoded ecf is thermoregulated via an intrinsically curved DNA while the chromosomal lpxM is regulated by the PhoP/Q two component regulatory system. However, it is unclear why E. coli O157: H7 carries two copies of LPS myristoyl transferase that are differentially regulated. In this study, a whole genome-scale transcriptome specific to E. coli O157:H7 was carried out for identification of the genes differentially expressed in the amyristoylated E. coli O157:H7. The results identified a total of 110 EHEC genes that were up- or down-regulated in the amyristoylated E. coli O157:H7 strain, including genes associated with virulence (26.36%), metabolism (20.91%), transport (10.91%), signal transduction (4.55%), genetic information processing (3.64%), stress response (2.73%), regulatory function (2.73%), motility/adherence (3.64%), cell envelope (2.73%), cell division (1.82%) and ORFs of unknown function (17.27%). Of particular interest, the expression of LEE pathogenicity island genes was significantly influenced by LPS structural defects.

본 연구는 농촌진흥청 국립축산과학원에서 사육중인 제주재래돼지와 랜드레이스의 상호교차교배를 통해 생산된 417두의 F2집단을 대상으로 성장형질(생시체중, 3주령 체중, 10주령 체중, 20주령 체중)을 측정하고, 개체별 혈액으로부터 Illumina Porcine SNP 60k BeadChip을 이용하여 유전자형 분석을 실시하여 성장형질과 유전체 전장의 단일염기다형의 유전자형 간에 연관성을 알아보았다. 단일연기다형의 유전자형 분석은 돼지의 성염색체를 제외한 18개의 상염색체 내에 나타난 52,574개의 SNP표지인자 중다형성이 나타나지 않은 7,564개의 표지인자, 모든 개체에서 이형으로 나타난 47개 표지인자 및 결측률이 10 % 이상인 1,830개의 표지인자가 나타나 분석에 앞서 사전 제거를 실시하였으며, 남은 44,133개의 표지인자를 체중형질과 표지인자간 연관성 분석하는데 이용하였다. 체중에 영향하는 고정효과에 대해 일반선형모형을 설정하여 사전 보정을 실시하였으며, 여기서 얻어진 잔차값을 이용하여 표지인자와 월령별 체중간의 연관성 분석을 실시하였다. 분석결과 전장의 유전체 정보 중 통계적 판단의 오류를 고려하여 연관성이 강한(p <10-6)표지인자가 생시(BWB), 3주령(BW3), 10주령(BW10) 및 20주령(BW20) 체중에서 각각 657개, 846개, 49개, 122개로 추정되었다. 생시와 3주령 체중에 공통으로 유의적 영향을 하는 표지인자가 286개로 나타났으며, BWB와 BW10에서 5개, BWB와 BW20에서 8개, BW3와 BW10에서 13개, BW3과 BW20에서 11개, BW10과 BW20에서 1개로 나타났다. 또한 염색체별 성장형질에 영향하는 표지인자의 분포를 조사한 결과, 주령별 체중에 영향하는 표지인자는 전장의 유전체에 고르게 분포하는 것으로 조사되었으며, 특히 생시 및 3주령 체중에 영향하는 표지인자는 특정 염색체(SSC9)에서 고도의 통계적 유의차(p <10-15)를 나타내는 유전자 좌위가 있는 것으로 추정되었다.

The application to genome study has been particularly developed with the introduction of the next-generation DNA sequencer (NGS) Roche/454 and Illumina/Solexa systems, along with bioinformation analysis technologies of whole-genome de novoassembly, expression profiling, DNA variation discovery, and genotyping. One of the advantages of the NGS systems is the cost-effectiveness to obtain the result of high-throughput DNA sequencing for genome, RNAnome, and miRNAnome studies. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing de novo assembly of novel genome sequencing data and for resequencing the samples with a reference genome DNA sequence. To construct high-quality contig consensus sequences, each DNA fragment read length is important to obtain de novo assembly with long reading sequences of the Roche/454 system. It is necessary to have DNA sequence information from a multiplatform NGS with at least 2× and 30×depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly, as hybrid assembly for novel genome sequencing would be cost-effective. In some cases, Illumina/Solexa data are used to construct scaffolds through de novo assembly with high coverage depth and large diverse fragment mate paired-end information,even though they are already participating in assembly and have made many contigs. Massive short-length reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. MAQ and CLC software are useful to both single nucleotide polymorphism discovery and genotyping through a comparison of resequencing data to a reference genome. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples, such as control and exposed tissue. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20× and 50× coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively,is effective to create novel expressed reference sequences. However, only an average 30× coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence. In an in silicomethod, conserved miRNA and novel miRNA discovery is available on massive miRNAnome data in any species. Particularly, the discovered target genes of miRNA could be robust to approach genome biology study.

The differences in the immune response between body lice, Pediculus humanus humanus, and head lice, Pediculus humanus capitis, were regarded as primary factors determining their differential vector competence. To find any differences in genetic components in immune system between body and head lice, whole genome sequences of head lice were determined by both SBS [sequencing by synthesis, Illumina Genome Analyzer (Illumina-GA)] and pyrosequencing (Roche GS FLX), and compared with the reference genome sequences of body lice. The short DNA reads from Illumina-GA (an average mapping depth of 50-fold) were aligned first to the body louse reference genome, to which Roche GS FLX DNA reads (an average depth of 2.5-fold) were subsequently assembled to make up gaps between mapped consensus. Total consensus showed a size of 114 Mb and a coverage of 96% of the published body louse genome sequences. From this head louse genome sequences, a total of 12,651 genes were predicted and used for comparing with the 10,775 genes previously reported from the body louse genome. The homolog analysis identified 873 head louse-specific genes and 422 body lice-specific genes. Comparison of immune response genes between both louse species showed head lice have more number of immune-related genes than body lice. Head lice were determined to possess all of the 107 immune-related genes reported in the previous study (Kim et al., 2011), suggesting that there is no difference in genetic make-up in terms of the 107 immune-related genes between body and head lice.