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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>
FISH SCHOOLING ANIMATION SYSTEM FOR CONSTRUCTING CONTENTS OF VIRTUAL UNDERWATER WORLD
Seungil Cho,Jongchan Kim,Cheeyong Kim,Eungkon Kim 한국멀티미디어학회 2007 한국멀티미디어학회 국제학술대회 Vol.2007 No.-
The goal of researching a proper crowd animation is to design system that is satisfied with the reality of scenes, performance of system, and interaction with users to show the crowd vividly and effectively in virtual underwater world. In this paper, we smartly expressed the behavior patterns for flocks offish in virtual underwater and we made up for the weak points in spending time and cost to produce crowd animation. We compared with the number of mesh, the number of fish, the number of frame, elapsed time, and resolution and analyzes them with the fish behavior simulating system. We developed a virtual underwater simulator using this system.
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>
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.
( Seungill Kim ),( Doil Choi ) 생화학분자생물학회(구 한국생화학분자생물학회) 2018 BMB Reports Vol.51 No.2
Long terminal repeat retrotransposons (LTR-Rs) are major elements creating new genome structure for expansion of plant genomes. However, in addition to the genome expansion, the role of LTR-Rs has been unexplored. In this study, we constructed new reference genome sequences of two pepper species (Capsicum baccatum and C. chinense), and updated the reference genome of C. annuum. We focused on the study for speciation of Capsicum spp. and its driving forces. We found that chromosomal translocation, unequal amplification of LTR-Rs, and recent gene duplications in the pepper genomes as major evolutionary forces for diversification of Capsicum spp. Specifically, our analyses revealed that the nucleotide-binding and leucine-rich-repeat proteins (NLRs) were massively created by LTR-R-driven retroduplication. These retoduplicated NLRs were abundant in higher plants, and most of them were lineage-specific. The retroduplication was a main process for creation of functional disease-resistance genes in Solanaceae plants. In addition, 4-10% of whole genes including highly amplified families such as MADS-box and cytochrome P450 emerged by the retroduplication in the plants. Our study provides new insight into creation of disease-resistance genes and high-copy number gene families by retroduplication in plants. [BMB Reports: Perspective 2018; 51(2): 55-56]