Author
Jonghoon Lee
Other affiliations: Konkuk University, Samsung
Bio: Jonghoon Lee is an academic researcher from Seoul National University. The author has contributed to research in topics: Genome & Genome evolution. The author has an hindex of 16, co-authored 51 publications receiving 1557 citations. Previous affiliations of Jonghoon Lee include Konkuk University & Samsung.
Papers published on a yearly basis
Papers
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Crops Research Institute1, Australian Centre for Plant Functional Genomics2, Agriculture and Agri-Food Canada3, Purdue University4, Plant Genome Mapping Laboratory5, Southwest University6, University of York7, Seoul National University8, Southern Cross University9, University of Missouri10, Centre national de la recherche scientifique11, Huazhong Agricultural University12, Hunan Agricultural University13, University of Queensland14, National Research Council15, Central University, India16, Sahmyook University17, King Abdulaziz University18
TL;DR: A draft genome sequence of Brassica oleracea is described, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks.
Abstract: Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear Brassica is an ideal model to increase knowledge of polyploid evolution Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B oleracea This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus
884 citations
TL;DR: A high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence is introduced, clarifying three ambiguous but important issues in the evolution of wild Oryza species.
Abstract: Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.
161 citations
TL;DR: Comparison of the present results with those of typical steady simulations showed that the difference in flow characteristics is magnified in the expiration phase, which may suggest that the inertial effect associated with unsteady flow is more important during the expiration period.
85 citations
TL;DR: The genotyping-by-sequencing (GBS) technique is applied to construct a high-resolution genetic map and identify clubroot resistance (CR) genes and reposition 37 and 2 misanchored scaffolds in the 02–12 and TO1000DH genome sequences, respectively.
Abstract: Clubroot is a devastating disease caused by Plasmodiophora brassicae and results in severe losses of yield and quality in Brassica crops. Many clubroot resistance genes and markers are available in Brassica rapa but less is known in Brassica oleracea. Here, we applied the genotyping-by-sequencing (GBS) technique to construct a high-resolution genetic map and identify clubroot resistance (CR) genes. A total of 43,821 SNPs were identified using GBS data for two parental lines, one resistant and one susceptible lines to clubroot, and 18,187 of them showed >5× coverage in the GBS data. Among those, 4,103 were credibly genotyped for all 78 F2 individual plants. These markers were clustered into nine linkage groups spanning 879.9 cM with an average interval of 1.15 cM. Quantitative trait loci (QTLs) survey based on three rounds of clubroot resistance tests using F2 : 3 progenies revealed two and single major QTLs for Race 2 and Race 9 of P. brassicae, respectively. The QTLs show similar locations to the previously reported CR loci for Race 4 in B. oleracea but are in different positions from any of the CR loci found in B. rapa. We utilized two reference genome sequences in this study. The high-resolution genetic map developed herein allowed us to reposition 37 and 2 misanchored scaffolds in the 02-12 and TO1000DH genome sequences, respectively. Our data also support additional positioning of two unanchored 3.3 Mb scaffolds into the 02-12 genome sequence.
78 citations
TL;DR: The near-complete chromosome sequence from a dicotyledonous crop species provides an example of the complexity of genome evolution following polyploidy and provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.
Abstract: Background
The species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species.
70 citations
Cited by
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Civil Aviation Authority of Singapore1, Rothamsted Research2, Beijing Institute of Genomics3, University of Copenhagen4, Rural Development Administration5, John Innes Centre6, North China University of Science and Technology7, University of Georgia8, University of California, Berkeley9, University of Missouri10, University of Queensland11, Australian Research Council12, National Research Council13, Bielefeld University14, Australian Centre for Plant Functional Genomics15, University of Rennes16, Wageningen University and Research Centre17, Agriculture and Agri-Food Canada18, Huazhong Agricultural University19, French Alternative Energies and Atomic Energy Commission20, Chungnam National University21, Norwich Research Park22
TL;DR: The annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage, and used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution.
Abstract: We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
1,811 citations
University of Évry Val d'Essonne1, Crops Research Institute2, Agriculture and Agri-Food Canada3, J. Craig Venter Institute4, Fujian Agriculture and Forestry University5, Plant Genome Mapping Laboratory6, University of Giessen7, French Alternative Energies and Atomic Energy Commission8, Institut national de la recherche agronomique9, National Research Council10, Australian Centre for Plant Functional Genomics11, University of Cologne12, Purdue University13, University of California, Berkeley14, University of British Columbia15, Fondation Jean Dausset Centre d'Etude du Polymorphisme Humain16, Huazhong Agricultural University17, Hunan Agricultural University18, Chungnam National University19, University of Arizona20, University of York21, University of Missouri22, Southern Cross University23, University of Western Australia24, Centre national de la recherche scientifique25
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Abstract: Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
1,743 citations
01 Jan 2009
TL;DR: This paper presents a meta-modelling framework for modeling and testing the robustness of the modeled systems and some of the techniques used in this framework have been developed and tested in the field.
Abstract: ing WS1S Systems to Verify Parameterized Networks . . . . . . . . . . . . 188 Kai Baukus, Saddek Bensalem, Yassine Lakhnech and Karsten Stahl FMona: A Tool for Expressing Validation Techniques over Infinite State Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204 J.-P. Bodeveix and M. Filali Transitive Closures of Regular Relations for Verifying Infinite-State Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220 Bengt Jonsson and Marcus Nilsson Diagnostic and Test Generation Using Static Analysis to Improve Automatic Test Generation . . . . . . . . . . . . . 235 Marius Bozga, Jean-Claude Fernandez and Lucian Ghirvu Efficient Diagnostic Generation for Boolean Equation Systems . . . . . . . . . . . . 251 Radu Mateescu Efficient Model-Checking Compositional State Space Generation with Partial Order Reductions for Asynchronous Communicating Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266 Jean-Pierre Krimm and Laurent Mounier Checking for CFFD-Preorder with Tester Processes . . . . . . . . . . . . . . . . . . . . . . . 283 Juhana Helovuo and Antti Valmari Fair Bisimulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299 Thomas A. Henzinger and Sriram K. Rajamani Integrating Low Level Symmetries into Reachability Analysis . . . . . . . . . . . . . 315 Karsten Schmidt Model-Checking Tools Model Checking Support for the ASM High-Level Language . . . . . . . . . . . . . . 331 Giuseppe Del Castillo and Kirsten Winter Table of
1,687 citations
10 Dec 2007
TL;DR: The experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Abstract: EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
1,528 citations
TL;DR: Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenomes, suggesting asymmetric evolution.
Abstract: Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.
1,221 citations