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Kim, Seungill,Kim, Myung-Shin,Kim, Yong-Min,Yeom, Seon-In,Cheong, Kyeongchae,Kim, Ki-Tae,Jeon, Jongbum,Kim, Sunggil,Kim, Do-Sun,Sohn, Seong-Han,Lee, Yong-Hwan,Choi, Doil Oxford University Press 2015 DNA research Vol.22 No.1
<P>The onion (<I>Allium cepa</I> L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from <I>de novo</I> sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and <I>ab initio</I> gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on <I>de novo</I> transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in <I>Allium</I> spp.</P>
Kim, Seungill,Park, Minkyu,Yeom, Seon-In,Kim, Yong-Min,Lee, Je Min,Lee, Hyun-Ah,Seo, Eunyoung,Choi, Jaeyoung,Cheong, Kyeongchae,Kim, Ki-Tae,Jung, Kyongyong,Lee, Gir-Won,Oh, Sang-Keun,Bae, Chungyun,Kim Nature Publishing Group, a division of Macmillan P 2014 Nature genetics Vol.46 No.3
Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.
Kim, Yong-Min,Kim, Seungill,Koo, Namjin,Shin, Ah-Young,Yeom, Seon-In,Seo, Eunyoung,Park, Seong-Jin,Kang, Won-Hee,Kim, Myung-Shin,Park, Jieun,Jang, Insu,Kim, Pan-Gyu,Byeon, Iksu,Kim, Min-Seo,Choi, JinH Oxford University Press 2017 DNA research Vol.24 No.1
<P><B>Abstract</B></P><P><I>Hibiscus syriacus</I> (L.) (rose of Sharon) is one of the most widespread garden shrubs in the world. We report a draft of the <I>H. syriacus</I> genome comprised of a 1.75 Gb assembly that covers 92% of the genome with only 1.7% (33 Mb) gap sequences. Predicted gene modeling detected 87,603 genes, mostly supported by deep RNA sequencing data. To define gene family distribution among relatives of <I>H. syriacus</I>, orthologous gene sets containing 164,660 genes in 21,472 clusters were identified by OrthoMCL analysis of five plant species, including <I>H. syriacus</I>, <I>Arabidopsis thaliana, Gossypium raimondii, Theobroma cacao</I> and <I>Amborella trichopoda.</I> We inferred their evolutionary relationships based on divergence times among Malvaceae plant genes and found that gene families involved in flowering regulation and disease resistance were more highly divergent and expanded in <I>H. syriacus</I> than in its close relatives, <I>G. raimondii</I> (DD) and <I>T. cacao</I>. Clustered gene families and gene collinearity analysis revealed that two recent rounds of whole-genome duplication were followed by diploidization of the <I>H. syriacus</I> genome after speciation. Copy number variation and phylogenetic divergence indicates that WGDs and subsequent diploidization led to unequal duplication and deletion of flowering-related genes in <I>H. syriacus</I> and may affect its unique floral morphology.</P>
Sujung Kim,Hualin Nie,Byungki Jun,Jiseong Kim,Jeongeun Lee,Seungill Kim,Ekyune Kim,Sunhyung Kim 한국유전학회 2020 Genes & Genomics Vol.42 No.5
Background Sweet potato is easily propagated by cuttings. But the molecular biological mechanism of adventitious root formation are not yet clear. Objective To understand the molecular mechanisms of adventitious root formation from stem cuttings in sweet potato. Methods RNA-seq analysis was performed using un-rooted stem (0 day) and rooted stem (3 days). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, comparison with Arabidopsis transcription factors (TFs) of DEGs were conducted to investigate the characteristics of genes and TFs involved in root formation. In addition, qRT-PCR analysis using roots at 0, 3, 6, 9, and 12 days after planting was performed to confirm RNA-seq reliability and related genes expression. Results 42,459 representative transcripts and 2092 DEGs were obtained through the RNA-seq analysis. The DEGs indicated the GO terms related to the single-organism metabolic process and cell periphery, and involved in the biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis in KEGG pathways. The comparison with Arabidopsis thaliana TF database showed that 3 TFs (WRKY, NAC, bHLH) involved in root formation of sweet potato. qRT-PCR analysis, which was conducted to confirm the reliability of RNA-seq analysis, indicated that some metabolisms including oxidative stress and wounding, transport, hormone may be involved in adventitious root formation. Conclusions The detected genes related to secondary metabolism, some hormone (auxin, gibberellin), transports, etc. and 3 TFs (WRKY, NAC, bHLH) may have functions in adventitious roots formation. This results provide valuable resources for future research on the adventitious root formation of sweet potato.
Lung Transplantation in Six Patients with Idiopathic Pulmonary Artery Hypertension
( Hyeonhwa Kim ),( Dongkwan Kim ),( Sehoon Choi ),( Geundong Lee ),( Dongkyu Oh ),( Hocheol Kim ),( Jaeseung Lee ),( Sungho Jung ),( Pilje Kang ),( Won Kim ),( Seungil Park ),( Sangbum Hong ) 대한결핵 및 호흡기학회 2021 대한결핵 및 호흡기학회 추계학술대회 초록집 Vol.129 No.0
Idiopathic pulmonary artery hypertension (IPAH) is an incurable and invariably fatal disease. Lung transplantation is a useful therapeutic option in patients who are unresponsive to medical treatment; however, lung transplantation performed for pulmonary hypertension is associated with significantly high perioperative mortality rates. We report a case series of six patients who underwent lung transplantation for IPAH between October 2008 and June 2021. Patients’ median age was 28.5 years, and the study included 5 of 6 women (83%). Pre-transplantation hemodynamic parameters showed mean right atrial pressure of 12.0±7.1 mmHg and mean pulmonary artery pressure of 62.2±29.5 mmHg. Two of six patients received extracorporeal membrane oxygenation (ECMO) therapy as a bridge to transplantation over 14 and 17 days, and four patients underwent elective transplantation. Two patients required prolonged postoperative venoarterial (V-A) ECMO support. Grade 3 primary graft dysfunction occurred in one patient; however, the clinical course improved following prolonged V-A ECMO therapy. Five patients (83.3%) required intervention for postoperative bleeding control; one of these patients died of uncontrolled bleeding concomitant with disseminated intravascular coagulation, on the 14th postoperative day, and we observed no other perioperative deaths. One patient died of carbapenem-resistant Acinetobacter baumannii bacteremia, a year postoperatively. The 1-month, 6-month, and 1-year survival rates were 83.3%, 83.3%, and 66.7%, respectively. In view of the poor prognosis of IPAH, lung transplantation (1-year mortality rates <40%) merits consideration as a useful therapeutic option in this patient population. However, postoperative bleeding tends to occur in most patients; therefore, close monitoring is important during post-transplantation management.
Ubiquitous Cyber Aquarium to Use Crowd Behavior
Seungil Cho,Jongchan Kim,Cheeyong Kim,Eungkon Kim 한국멀티미디어학회 2008 한국멀티미디어학회 국제학술대회 Vol.2008 No.-
Recently, representing the crowd environment in animation becomes a hot issue to the digital entertainment industry. The goal of proper digital crowd animation is to design characters in animation that are defined by the reality of scenes, performance of system and interaction with users to show the crowd vividly and effectively in cyber underwater. In this paper, we implement a realistic 3D cyber aquarium using crowd animation and construct the aquarium to disappear the fish on screen after recognizing the approaching distance through supersonic distance sensor.