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( 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]
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.
Genome-wide identification of pepper NB-LRR gene family and their evolutionary history in Solanaceae
Eunyoung Seo,Seon-In Yeom,Seungill Kim,Joohyun Lee,Saet-Byul Kim,Eunbi Choi,Eun Hye Choi,Doil Choi 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Plants have evolved elaborate innate immune systems against invading pathogens, such as bacteria, fungi, oomycetes, viruses and insects. Among them, intracellular immune receptors known as nucleotide-binding site and leucine-rich repeat (NB-LRR) play critical roles in effector-triggered immunity (ETI) regarding to plant defense. Here, we identified potential NB-LRR coding sequences from pepper genome using bioinformatics analysis and performed comparative analysis with Solanaceae plants. As a result, we identified 267, 443, and 755 NBS-encoding genes in the genome of tomato, potato, and pepper, respectively. These may indicate that the Solanaceae NB-LRRs were evolved through species-specific unequal-duplication event. Further phylogenetic and clustering analyses revealed that Solanaceae NB-LRRs were classified into the 14 subgroups with 1 TNL and 13 CNL types. We found that the genes in CNL-G1 and CNL-G2 subgroup were highly expanded compared to other subgroup showing a large portion of NB-LRR in pepper genome. Among 755 NB-LRRs in pepper genome, 623 were physically mapped on all 12 pepper chromosome pseudomolecules. Furthermore, a number of NB-LRRs in the same group were physically clustered by tandem array in the specific chromosome. Genome-wide identification of pepper NB-LRR family and their evolutionary analysis could provide an important resource for identification and characterization of genes for breeding of disease resistance crops.
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>
길혜민(Hyemin Kil),양승일(Seungill Yang) 한국부동산산업학회 2022 부동산산업연구 Vol.5 No.1
본 연구는 1인 가구 증가와 더불어 코로나19 사태로 유통산업 환경이 급변하면서 시장규모의 증가로 유통시장이 성장함에 따라 물류시설의 수요 증가에 따른 공급도 확대되고 있다. 이에 물류창고가 가장 많이 밀집되어 있는 경기도의 남부권 물류창고 부지의 사업성분석을 통하여 안정적인 물동량 확보 및 최적의 물류서비스의 공급 방향을 제시하고자 한다. 첫째, 수도권 물류센터는 국내 물류센터의 약 60%를 차지하며 2018년부터 급격히 늘어나며, 전통적 물류창고 집적지역인 동남권의 경우 공급은 지속적으로 증가하고 있으며, 최근 서부권에도 공급이 증가하고 있어 수도권으로의 양호한 교통 환경조건이 교차하는 곳인 안성시 또한 물류·유통에 대한 수요가 높아 물류시설의 입지에 매우 유리한 지역으로 전망된다. 둘째, 코로나19로 인한 비대면 온라인매출의 증가와 신선식품 시장의 급성장 등 수도권의 물류 수요 급증으로 인해 도로 인프라 활용이 용이한 지역을 중심으로 물류시설의 공급이 요구되고 있다. 1인 가구의 증가 및 코로나19로 인한 비대면 소비문화의 변화로 냉동·냉장의 신선식품 소비가 급격하게 증가하고 있으며, 1인 가구의 46.98%가 밀집되어 있는 수도권에 냉동·냉장 시설의 수요가 급증하고 있다. 그러나 냉동·냉장창고는 2023년으로 갈수록 임차인 확보에 어려움을 겪을 것으로 예상되어 신규 공급에 유의해야 한다. 셋째, 앞으로도 물류창고는 기관 투자자의 주요투자자산으로 선호가 지속될 것으로 전망되나 부지확보와 인허가의 어려움, ESG 강화 등의 변화로 공급에 제약요인이 커지고 있어 향후 정기적 관점의 공급이 이루어져야 할 것으로 판단된다. This study tries to analyze the business feasibility of the logistics warehouse land in the southern area of Gyeonggi-do, where there is the highest density of logistics warehouses, and to suggest the directions for securing a stable quantity of goods and providing an optimal distribution service. Firstly, the logistics centers in the metropolitan areas account for about 60% of domestics ones, and have been on the sharp rise since 2018. In the case of the south eastern area where traditional logistics warehouses are concentrated, the supply of logistics facilities has been on the constant rise. Recently, supply in the western area is also on the increase. Anseong, the city that meets good conditions of traffic to the metropolitan areas, faces high demands of logistics and distribution. Given that, the city is expected to have an advantageous position for logistics facilities. Secondly, the COVID-19 pandemic led to a rise in non-contact online sales and the rapid growth of the market of fresh food products. Unfortunately, it is predicted that it is hard to secure lessees of freezing and chilling warehouses in 2023. Therefore, it is necessary to pay attention to new supply. Thirdly, logistics warehouses are expected to become favorable investment assets of institutional investors continuously. However, as more restrictions on supply are made by difficulties in securing land and permission and enhanced SG, it is necessary to achieve regular supply.