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Eukaryotic DNAJ/K Database: A Comprehensive Phylogenomic Analysis Platform for the DNAJ/K Family
Cheong, Kyeongchae,Choi, Jaehyuk,Choi, Jaeyoung,Park, Jongsun,Jang, Suwang,Lee, Yong-Hwan Korea Genome Organization 2013 Genomics & informatics Vol.11 No.1
Proteins in DNAJ/K families are ubiquitous, from prokaryotes to eukaryotes, and function as molecular chaperones. For systematic phylogenomics of the DNAJ/K families, we developed the Eukaryotic DNAJ/K Database (EDD). A total of 12,908 DNAJs and 4,886 DNAKs were identified from 339 eukaryotic genomes in the EDD. Kingdom-wide comparison of DNAJ/K families provides new insights on the evolutionary relationship within these families. Empowered by 'class', 'cluster', and 'taxonomy' browsers and the 'favorite' function, the EDD provides a versatile platform for comparative genomic analyses of DNAJ/K families.
Choi, Jaeyoung,Cheong, Kyeongchae,Jung, Kyongyong,Jeon, Jongbum,Lee, Gir-Won,Kang, Seogchan,Kim, Sangsoo,Lee, Yin-Won,Lee, Yong-Hwan Oxford University Press 2013 Nucleic acids research Vol.41 No.d1
<P>In 2007, Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr/) was publicly open with 65 genomes corresponding to 58 fungal and Oomycete species. The CFGP provided six bioinformatics tools, including a novel tool entitled BLASTMatrix that enables search homologous genes to queries in multiple species simultaneously. CFGP also introduced Favorite, a personalized virtual space for data storage and analysis with these six tools. Since 2007, CFGP has grown to archive 283 genomes corresponding to 152 fungal and Oomycete species as well as 201 genomes that correspond to seven bacteria, 39 plants and 105 animals. In addition, the number of tools in Favorite increased to 27. The Taxonomy Browser of CFGP 2.0 allows users to interactively navigate through a large number of genomes according to their taxonomic positions. The user interface of BLASTMatrix was also improved to facilitate subsequent analyses of retrieved data. A newly developed genome browser, Seoul National University Genome Browser (SNUGB), was integrated into CFGP 2.0 to support graphical presentation of diverse genomic contexts. Based on the standardized genome warehouse of CFGP 2.0, several systematic platforms designed to support studies on selected gene families have been developed. Most of them are connected through Favorite to allow of sharing data across the platforms.</P>
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>
Genome Sequence of <i>Striga asiatica</i> Provides Insight into the Evolution of Plant Parasitism
Yoshida, Satoko,Kim, Seungill,Wafula, Eric K.,Tanskanen, Jaakko,Kim, Yong-Min,Honaas, Loren,Yang, Zhenzhen,Spallek, Thomas,Conn, Caitlin E.,Ichihashi, Yasunori,Cheong, Kyeongchae,Cui, Songkui,Der, Jos Elsevier 2019 Current biology Vol.29 No.18
<P><B>Summary</B></P> <P>Parasitic plants in the genus <I>Striga</I>, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of <I>Striga</I> parasite biology, which could lead to agricultural solutions, has been hampered by the lack of genome information. Here, we report the draft genome sequence of <I>Striga asiatica</I> with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. <I>Striga</I> seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialized penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among <I>Striga</I> spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in <I>Striga</I>, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to <I>S. asiatica</I> from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of <I>Striga</I> control strategies.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The <I>Striga</I> genome reflects a three-phase model of parasitic plant genome evolution </LI> <LI> A family of strigolactone receptors has undergone a striking expansion in <I>Striga</I> </LI> <LI> Genes in lateral root development are coordinately induced in a parasitic organ </LI> <LI> Host genes and retrotransposons are horizontally transferred into <I>Striga</I> </LI> </UL> </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.