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Jung, Hyungtaek,Yoon, Byung-Ha,Kim, Woo-Jin,Kim, Dong-Wook,Hurwood, David A.,Lyons, Russell E.,Salin, Krishna R.,Kim, Heui-Soo,Baek, Ilseon,Chand, Vincent,Mather, Peter B.,Lin, Li MDPI AG 2016 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.17 No.5
<P>The giant freshwater prawn, <I>Macrobrachium rosenbergii</I>, a sexually dimorphic decapod crustacean is currently the world’s most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the <I>M. rosenbergii</I> sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from <I>M. rosenbergii</I> applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple <I>k</I>-mer methods respectively, were used to analyse the data. The influence of multiple <I>k</I>-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, <I>de novo</I> assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in <I>M. rosenbergii</I>, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on <I>M</I>. <I>rosenbergii</I> and can be applied more widely on other freshwater prawn species in the genus <I>Macrobrachium</I>.</P>
Kim, Woo-Jin,Jung, Hyungtaek,Shin, Eun-Ha,Baek, Ilseon The Malacological Society of Korea 2014 The Korean Journal of Malacology Vol.30 No.3
Single nucleotide polymorphisms (SNPs) are widely acknowledged as the marker of choice for many genetic and genomic applications because they show co-dominant inheritance, are highly abundant across genomes and are suitable for high-throughput genotyping. Here we evaluated the applicability of SNP markers developed from Crassostrea gigas and C. virginica expressed sequence tags (ESTs) in closely related Crassostrea and Ostrea species. A total of 213 putative interspecific level SNPs were identified from re-sequencing data in six amplicons, yielding on average of one interspecific level SNP per seven bp. High polymorphism levels were observed and the high success rate of transferability show that genic EST-derived SNP markers provide an efficient method for rapid marker development and SNP discovery in closely related oyster species. The six EST-SNP markers identified here will provide useful molecular tools for addressing questions in molecular ecology and evolution studies including for stock analysis (pedigree monitoring) in related oyster taxa.
성인에서의 병적 위치 변형이 없는 아킬레스건 종골 후방 부착부의 특징: 자기공명영상 계측 연구
곽희철,정대원,박형택,하동준,곽재용,김의철,Gwak, Heuichul,Jung, Daewon,Park, Hyungtaek,Ha, Dongjun,Kwak, Jaeyong,Kim, Uicheol 대한족부족관절학회 2016 대한족부족관절학회지 Vol.20 No.3
Purpose: We aimed to investigate the safety zone for Achilles tendon insertion in the posterior aspect of the calcaneus via the use of magnetic resonance imaging (MRI) when planning for insertional Achilles tendinopathy. Materials and Methods: This study included 95 patients. The MRI of midsagittal plane of the ankle joint was used to measure the proximal and distal insertion point for the Achilles tendon in the posterior aspect of the calcaneus. Patients were divided into three groups according to the proportion of the distal insertion point out of the entire calcaneal length: the proximal, middle, and distal insertion groups. Results: The mean proximal and distal insertion points for the Achilles tendon were measured as 1.05 cm (0~2.11 cm) and 2.36 cm (1.60~2.93 cm), respectively. When the posterior aspect of the calcaneus was used as the reference plane, none of the patients was in the proximal insertion group, while 75 and 20 patients were in the middle and distal insertion groups, respectively. The insertion portion was longer in the distal insertion group ($1.47{\pm}0.25cm$) than in the middle insertion group ($1.27{\pm}0.35cm$). Statistically significant differences with respect to the length of the insertion portion were observed between the two groups (p=0.008). Conclusion: Removal of more than 1 cm below the superior margin of the posterior calcaneus may be dangerous. An MRI study on the Achilles tendon of patients without hindfoot deformity or tendinopathy revealed various insertional characteristics. Preoperative MRI evaluation is safer than relying solely on the simple radiological assessment when planning for insertional Achilles tendinopathy.
Transcriptome profiling of olive flounder responses under acute and chronic heat stress
Woo‑Jin Kim,이규빈,Dain Lee,Hyun‑Chul Kim,Bo‑Hye Nam,Hyungtaek Jung,이선주,Kyunghwan Kim 한국유전학회 2021 Genes & Genomics Vol.43 No.2
Background The olive founder (Paralichthys olivaceus) is a saltwater fsh, which is valuable to the economy. The olive founder strives to adapt to environmental stressors through physiological, biochemical, and transcriptional responses. The rise in water temperature threatens the growth, development, reproduction, and survival of olive founder. Each organ in the olive founder can diferentially respond to heat stress. Objectives The purpose of this study is to investigate organ-specifc transcriptional changes in olive founder tissues during heat stress. Methods In this study, transcriptome dynamics of the gill, liver, and muscle of olive founder to acute or chronic heat stress were investigated. Results Principal component analysis plotting revealed that the transcriptome of each organ is quite separated. K-means clustering, gene ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed the diferential transcriptome responses of each organ to heat stress. Heat stress commonly afects the pathways involved in the correct protein folding, DNA repair, and cell cycle. Conclusion Our results may provide a valuable molecular basis of heat acclimation in fshes.
Kim, Woo-Jin,Shin, Eun-Ha,Kong, Hee Jeong,Nam, Bo-Hye,Kim, Young-Ok,Jung, Hyungtaek,An, Cheul Min The Korean Society of Fisheries and Aquatic Scienc 2013 Fisheries and Aquatic Sciences Vol.16 No.4
Microsatellite markers are important for gene mapping and for marker-assisted selection. Sixty-five polymorphic microsatellite markers were developed with an enriched partial genomic library from olive flounder Paralichthys olivaceus an important commercial fish species in Korea. The variability of these markers was tested in 30 individuals collected from the East Sea (Korea). The number of alleles for each locus ranged from 2 to 33 (mean, 17.1). Observed and expected heterozygosity as well as polymorphism information content varied from 0.313 to 1.000 (mean, 0.788), from 0.323 to 0.977 (mean, 0.820), and from 0.277 to 0.960 (mean, 0.787), respectively. Nine loci showed significant deviation from the Hardy-Weinberg equilibrium after sequential Bonferroni correction. Analysis with MICROCHECKER suggested the presence of null alleles at five of these loci with estimated null allele frequencies of 0.126-0.285. These new microsatellite markers from genomic libraries will be useful for constructing a P. olivaceus linkage map.
Eun-Ha Shin(신은하),Hee Jeong Kong(공희정),Bo-Hye Nam(남보혜),Young-Ok Kim(김영옥),Bong-Seok Kim(김봉석),Dong-Gyun Kim(김동균),Cheul Min An(안철민),Hyungtaek Jung(정형택),Woo-Jin Kim(김우진) 한국생명과학회 2015 생명과학회지 Vol.25 No.12
대하(Fenneropenaeus chinensis)는 우리나라에서 경제적으로 가장 중요한 양식생물 중 하나이다. 그러나 대하의 유전적 특성에 대한 연구는 전무하다. 본 연구에서는 새로 개발된 13개 미세위성체 유전자좌를 이용하여 우리나라에 서식하는 4개 지역 대하의 유전 다양성 및 집단간 관련성을 분석하였다. 평균 대립유전자 richness =16.87, 평균 이형접합률 =0.845를 보여 유전 다양성은 비교적 높은 수준을 보였다. 52개 유전좌중에서 13개 유전자좌가 집단간 분석에서 Hardy–Weinberg 평형에서 유의적인 차이로 벗어났다. Neighbor-joining, principal coordinate 및 molecular variance 분석 결과로 우리나라 대하 집단은 3개 집단(나라도, 천수만, 법성포 및 채석포)으로 구성되어 있으며, 이 결과는 유전적 거리에 근거한 군집 결과와 일치하였다. 본 연구에서 조사된 유전 다양성 및 분화결과는 앞으로 대하의 지속 가능한 자원관리 및 선발 육종을 통한 유전적 개량에 적용될 수 있을 것이다. The fleshy shrimp, Fenneropenaeus chinensis, is the family of Penaeidae and one of the most economically important marine culture species in Korea. However, its genetic characteristics have never been studied. In this study, a total of 240 wild F. chinensis individuals were collected from four locations as follows: Narodo (NRD, n = 60), Beopseongpo (BSP, n = 60), Chaesukpo (CSP, n = 60), and Cheonsuman (CSM, n = 60). Genetic variability and the relationships among four wild F. chinensis populations were analyzed using 13 newly developed microsatellite loci. Relatively high levels of genetic variability (mean allelic richness = 16.87; mean heterozygosity = 0.845) were found among localities. Among the 52 population loci, 13 showed significant deviation from the Hardy–Weinberg equilibrium. Neighbor-joining, principal coordinate, and molecular variance analyses revealed the presence of three subpopulations (NRD, CSM, BSP and CSP), which was consistent with clustering based on genetic distance. The mean observed heterozygosity values of the NRD, CSM, BSP, and CSP populations were 0.724, 0.821, 0.814, and 0.785 over all loci, respectively. These genetic variability and differentiation results of the four wild populations can be applied for future genetic improvement using selective breeding and to design suitable management guidelines for Korean F. chinensis culture.