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Beom-Seok Park

Bio: Beom-Seok Park is an academic researcher from Rural Development Administration. The author has contributed to research in topics: Genome & Brassica rapa. The author has an hindex of 30, co-authored 66 publications receiving 4639 citations. Previous affiliations of Beom-Seok Park include National Academy of Agricultural Sciences & Kyungpook National University.


Papers
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Journal ArticleDOI
Xiaowu Wang1, Hanzhong Wang, Jun Wang2, Jun Wang3, Jun Wang4, Rifei Sun, Jian Wu, Shengyi Liu, Yinqi Bai3, Jeong-Hwan Mun5, Ian Bancroft6, Feng Cheng, Sanwen Huang, Xixiang Li, Wei Hua, Junyi Wang3, Xiyin Wang7, Xiyin Wang8, Michael Freeling9, J. Chris Pires10, Andrew H. Paterson8, Boulos Chalhoub, Bo Wang3, Alice Hayward11, Alice Hayward12, Andrew G. Sharpe13, Beom-Seok Park5, Bernd Weisshaar14, Binghang Liu3, Bo Li3, Bo Liu, Chaobo Tong, Chi Song3, Chris Duran12, Chris Duran15, Chunfang Peng3, Geng Chunyu3, Chushin Koh13, Chuyu Lin3, David Edwards15, David Edwards12, Desheng Mu3, Di Shen, Eleni Soumpourou6, Fei Li, Fiona Fraser6, Gavin C. Conant10, Gilles Lassalle16, Graham J.W. King2, Guusje Bonnema17, Haibao Tang9, Haiping Wang, Harry Belcram, Heling Zhou3, Hideki Hirakawa, Hiroshi Abe, Hui Guo8, Hui Wang, Huizhe Jin8, Isobel A. P. Parkin18, Jacqueline Batley12, Jacqueline Batley11, Jeong-Sun Kim5, Jérémy Just, Jianwen Li3, Jiaohui Xu3, Jie Deng, Jin A Kim5, Jingping Li8, Jingyin Yu, Jinling Meng19, Jinpeng Wang7, Jiumeng Min3, Julie Poulain20, Katsunori Hatakeyama, Kui Wu3, Li Wang7, Lu Fang, Martin Trick6, Matthew G. Links18, Meixia Zhao, Mina Jin5, Nirala Ramchiary21, Nizar Drou22, Paul J. Berkman12, Paul J. Berkman15, Qingle Cai3, Quanfei Huang3, Ruiqiang Li3, Satoshi Tabata, Shifeng Cheng3, Shu Zhang3, Shujiang Zhang, Shunmou Huang, Shusei Sato, Silong Sun, Soo-Jin Kwon5, Su-Ryun Choi21, Tae-Ho Lee8, Wei Fan3, Xiang Zhao3, Xu Tan8, Xun Xu3, Yan Wang, Yang Qiu, Ye Yin3, Yingrui Li3, Yongchen Du, Yongcui Liao, Yong Pyo Lim21, Yoshihiro Narusaka, Yupeng Wang7, Zhenyi Wang7, Zhenyu Li3, Zhiwen Wang3, Zhiyong Xiong10, Zhonghua Zhang 
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

Journal ArticleDOI
TL;DR: A draft genome sequence of mungbean is constructed to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species.
Abstract: Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

397 citations

Journal ArticleDOI
TL;DR: Evidence is shown for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5.
Abstract: Strong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred ∼0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.

227 citations

Journal ArticleDOI
01 Dec 2007-Genetics
TL;DR: The number of QTL, interacting loci, and aligned functional genes revealed a complex genetic network controlling flowering time in B. napus.
Abstract: Most agronomical traits exhibit quantitative variation, which is controlled by multiple genes and are environmentally dependent. To study the genetic variation of flowering time in Brassica napus, a DH population and its derived reconstructed F(2) population were planted in 11 field environments. The flowering time varied greatly with environments; 60% of the phenotypic variation was attributed to genetic effects. Five to 18 QTL at a statistically significant level (SL-QTL) were detected in each environment and, on average, two new SL-QTL were discovered with each added environment. Another type of QTL, micro-real QTL (MR-QTL), was detected repeatedly from at least 2 of the 11 environments; resulting in a total of 36 SL-QTL and 6 MR-QTL. Sixty-three interacting pairs of loci were found; 50% of them were involved in QTL. Hundreds of floral transition genes in Arabidopsis were aligned with the linkage map of B. napus by in silico mapping; 28% of them aligned with QTL regions and 9% were consistent with interacting loci. One locus, BnFLC10, in N10 and a QTL cluster in N16 were specific to spring- and winter-cropped environments respectively. The number of QTL, interacting loci, and aligned functional genes revealed a complex genetic network controlling flowering time in B. napus.

207 citations

Journal ArticleDOI
TL;DR: It appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.
Abstract: Brassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics. We assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago. This work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.

201 citations


Cited by
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Journal ArticleDOI
Xun Xu1, Shengkai Pan1, Shifeng Cheng1, Bo Zhang1, Mu D1, Peixiang Ni1, Gengyun Zhang1, Shuang Yang1, Ruiqiang Li1, Jun Wang1, Gisella Orjeda2, Frank Guzman2, Torres M2, Roberto Lozano2, Olga Ponce2, Diana Martinez2, De la Cruz G3, Chakrabarti Sk3, Patil Vu3, Konstantin G. Skryabin4, Boris B. Kuznetsov4, Nikolai V. Ravin4, Tatjana V. Kolganova4, Alexey V. Beletsky4, Andrey V. Mardanov4, Di Genova A5, Dan Bolser5, David M. A. Martin5, Li G, Yang Y, Hanhui Kuang6, Hu Q6, Xiong X7, Gerard J. Bishop8, Boris Sagredo, Nilo Mejía, Zagorski W9, Robert Gromadka9, Jan Gawor9, Pawel Szczesny9, Sanwen Huang, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Youjun Zhang, Xie B, Du Y, Qu D, Merideth Bonierbale10, Marc Ghislain10, Herrera Mdel R, Giovanni Giuliano, Marco Pietrella, Gaetano Perrotta, Paolo Facella, O'Brien K11, Sergio Enrique Feingold, Barreiro Le, Massa Ga, Luis Aníbal Diambra12, Brett R Whitty13, Brieanne Vaillancourt13, Lin H13, Alicia N. Massa13, Geoffroy M13, Lundback S13, Dean DellaPenna13, Buell Cr14, Sanjeev Kumar Sharma14, David Marshall14, Robbie Waugh14, Glenn J. Bryan14, Destefanis M15, Istvan Nagy15, Dan Milbourne15, Susan Thomson16, Mark Fiers16, Jeanne M. E. Jacobs16, Kåre Lehmann Nielsen17, Mads Sønderkær17, Marina Iovene18, Giovana Augusta Torres18, Jiming Jiang18, Richard E. Veilleux19, Christian W. B. Bachem20, de Boer J20, Theo Borm20, Bjorn Kloosterman20, van Eck H20, Erwin Datema20, Hekkert Bt20, Aska Goverse20, van Ham Rc20, Richard G. F. Visser20 
10 Jul 2011-Nature
TL;DR: The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin.
Abstract: Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

1,813 citations

Journal ArticleDOI
Xiaowu Wang1, Hanzhong Wang, Jun Wang2, Jun Wang3, Jun Wang4, Rifei Sun, Jian Wu, Shengyi Liu, Yinqi Bai4, Jeong-Hwan Mun5, Ian Bancroft6, Feng Cheng, Sanwen Huang, Xixiang Li, Wei Hua, Junyi Wang4, Xiyin Wang7, Xiyin Wang8, Michael Freeling9, J. Chris Pires10, Andrew H. Paterson7, Boulos Chalhoub, Bo Wang4, Alice Hayward11, Alice Hayward12, Andrew G. Sharpe13, Beom-Seok Park5, Bernd Weisshaar14, Binghang Liu4, Bo Li4, Bo Liu, Chaobo Tong, Chi Song4, Chris Duran15, Chris Duran11, Chunfang Peng4, Geng Chunyu4, Chushin Koh13, Chuyu Lin4, David Edwards11, David Edwards15, Desheng Mu4, Di Shen, Eleni Soumpourou6, Fei Li, Fiona Fraser6, Gavin C. Conant10, Gilles Lassalle16, Graham J.W. King3, Guusje Bonnema17, Haibao Tang9, Haiping Wang, Harry Belcram, Heling Zhou4, Hideki Hirakawa, Hiroshi Abe, Hui Guo7, Hui Wang, Huizhe Jin7, Isobel A. P. Parkin18, Jacqueline Batley11, Jacqueline Batley12, Jeong-Sun Kim5, Jérémy Just, Jianwen Li4, Jiaohui Xu4, Jie Deng, Jin A Kim5, Jingping Li7, Jingyin Yu, Jinling Meng19, Jinpeng Wang8, Jiumeng Min4, Julie Poulain20, Katsunori Hatakeyama, Kui Wu4, Li Wang8, Lu Fang, Martin Trick6, Matthew G. Links18, Meixia Zhao, Mina Jin5, Nirala Ramchiary21, Nizar Drou22, Paul J. Berkman15, Paul J. Berkman11, Qingle Cai4, Quanfei Huang4, Ruiqiang Li4, Satoshi Tabata, Shifeng Cheng4, Shu Zhang4, Shujiang Zhang, Shunmou Huang, Shusei Sato, Silong Sun, Soo-Jin Kwon5, Su-Ryun Choi21, Tae-Ho Lee7, Wei Fan4, Xiang Zhao4, Xu Tan7, Xun Xu4, Yan Wang, Yang Qiu, Ye Yin4, Yingrui Li4, Yongchen Du, Yongcui Liao, Yong Pyo Lim21, Yoshihiro Narusaka, Yupeng Wang8, Zhenyi Wang8, Zhenyu Li4, Zhiwen Wang4, Zhiyong Xiong10, Zhonghua Zhang 
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

Journal ArticleDOI
Boulos Chalhoub1, Shengyi Liu2, Isobel A. P. Parkin3, Haibao Tang4, Haibao Tang5, Xiyin Wang6, Julien Chiquet1, Harry Belcram1, Chaobo Tong2, Birgit Samans7, Margot Correa8, Corinne Da Silva8, Jérémy Just1, Cyril Falentin9, Chu Shin Koh10, Isabelle Le Clainche1, Maria Bernard8, Pascal Bento8, Benjamin Noel8, Karine Labadie8, Adriana Alberti8, Mathieu Charles9, Dominique Arnaud1, Hui Guo6, Christian Daviaud, Salman Alamery11, Kamel Jabbari1, Kamel Jabbari12, Meixia Zhao13, Patrick P. Edger14, Houda Chelaifa1, David C. Tack15, Gilles Lassalle9, Imen Mestiri1, Nicolas Schnel9, Marie-Christine Le Paslier9, Guangyi Fan, Victor Renault16, Philippe E. Bayer11, Agnieszka A. Golicz11, Sahana Manoli11, Tae-Ho Lee6, Vinh Ha Dinh Thi1, Smahane Chalabi1, Qiong Hu2, Chuchuan Fan17, Reece Tollenaere11, Yunhai Lu1, Christophe Battail8, Jinxiong Shen17, Christine Sidebottom10, Xinfa Wang2, Aurélie Canaguier1, Aurélie Chauveau9, Aurélie Bérard9, G. Deniot9, Mei Guan18, Zhongsong Liu18, Fengming Sun, Yong Pyo Lim19, Eric Lyons20, Christopher D. Town4, Ian Bancroft21, Xiaowu Wang, Jinling Meng17, Jianxin Ma13, J. Chris Pires22, Graham J.W. King23, Dominique Brunel9, Régine Delourme9, Michel Renard9, Jean-Marc Aury8, Keith L. Adams15, Jacqueline Batley24, Jacqueline Batley11, Rod J. Snowdon7, Jörg Tost, David Edwards11, David Edwards24, Yongming Zhou17, Wei Hua2, Andrew G. Sharpe10, Andrew H. Paterson6, Chunyun Guan18, Patrick Wincker25, Patrick Wincker1, Patrick Wincker8 
22 Aug 2014-Science
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

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

Journal ArticleDOI
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