Mun Lab – Plant Genomes, Functions, & Evolutions

Introduction

Flowering plants (Angiosperms) have experienced diverse evolutionary changes since their sudden appearance in the fossil records of the Cretaceous period. The apparent genomic changes identified from angiosperms include genome expansion through polyploidy and functional diversification of duplicated genes. We are studying the structural and functional characteristics of the model, crop, or wild plant genomes using genetics, genomics, and bioinformatics tools. Our research interests are described as follow.

Research

Brassicaceae crops

The Brassicaceae family includes approximately 3,700 species in the 350 genera. The species have diverse characteristics; many of which are of agronomic importance as vegetables, condiments, fodder, and oil crops. Economically, the Brassicaceae species contribute to approximately 10% of the world’s vegetable crop produce and approximately 12% of the worldwide edible oil supplies. Species of particular interests to our research are Brassica rapa and Raphanus sativus as leaf or root vegetable crops in the tribe Brassiceae. They are sibling species with a triplicated genome structure. We investigate the speciation, domestication, and evolution of these species based on comparative analysis with their sequenced genomes.

Legumes are able to establish nitrogen-fixing symbioses with rhizobial bacteria. This mutualistic interaction is tightly controlled by the host plant via the nodulation signaling pathway. We explore the molecular nature of symbiotic signal transduction systems in the model legume Medicago truncatula using diverse methodologies including molecular genetics, stable transformation, and genome editing.

Genome sequencing of crop species has been facilitated by the introduction of next generation sequencing technologies that enable individual research groups to sequence and assemble the entire genome of interest. However, heterozygous plant genomes of natural trees or wild plants still pose considerable challenges in genome sequencing and assembly. We employ diverse approaches from molecular biology, genomics, and bioinformatics to elucidate the genome structure of wild plant species with economic or biological values.

Professor

Jeong-Hwan Mun

Professor

Dept. Bioscience and Bioinformatics

Myongji University, Korea

Email: munjh@mju.ac.kr

Graduate Students

Ara Cho

Ph.D. Student

Myongji University, Korea

Email: arajo0514@naver.com

Hoyeol Jang

Ph.D. Student

Myongji University, Korea

Email: ghduf1111@gmail.com

Moonjin Kim

Ph.D. Student

Myongji University, Korea

Email: yourme505@naver.com

Seunghoon Jung

Ph.D. Student

Myongji University, Korea

Email: jshjsh517@naver.com

Alumni

Young-Eun Kwon

M.S.

Email: yug9952@naver.com

Goon-Bo Kim

Research Professor

Email: goonbokim@gmail.com

Seung-Hoon Baek

Ph.D.

Email: yohanbosco@gmail.com

Seong-uk Son

M.S.

Email: seongukson@naver.com

Publications

Cho A, Jang H, Baek S, Kim M-J, Yim B, Huh S, Kwon S-H, Yu H-J, Mun J-H (2022) An improved Raphanus sativus cv. WK10039 genome localizes centromeres, uncovers variation of DNA methylation and resolves arrangement of the ancestral Brassica genome blocks in radish chromosomes. Theor Appl Genet 135:1731-1750

Kim G-B, Lim CE, Kim J-S, Kim K, Lee JH, Yu H-J, Mun J-H (2020) Comparative chloroplast genome analysis of Artemisia (Asteracae) in East Asia: insights into evolutionary divergence and phylogenomic implications. BMC Genomics 21: 415

Mun J-H, Yim B, Park SH, Shim HR, Kim J-H, Hur YY, Yu H-J (2020) Anatomical, biochemical and transcriptome analyses of Vitis vinifera cv. 'Hongju' reveal novel information regarding the seed hardness of stenospermocarpic soft-seed grapes. Plant Breed 139: 672-683

Yu H-J, Jeong Y-M, Lee Y-J, Yim B, Cho A, Mun J-H (2020) Marker integration and development of Fluidigm/KASP assays for high-throughput genotyping of radish. Hort Environ Biotechnol 61: 767-777

Larrainzar E, Millar I, Rubio MC, Pérez‐Rontomé C, Huertas R, Sato S, Mun J-H, Becana M (2020) Hemoglobins in the legume-Rhizobium symbiosis. New Phytol 228: 472-484

Kim C, Kim C-S, Mun J-H, Kim J-H (2019) Epitypification of Prunus × nudiflora (Rosaceae), a natural hybrid species in Jeju Island, Korea. J Asia-Pacific Biodiversity 12: 718-720

Kim G-B, Son S-U, Yu H-J, Mun J-H (2019) MtGA2ox10 encoding C20-GA2-oxidase regulates rhizobial infection and nodule development in Medicago truncatula. Sci Rep 9: 5952.​

Yu H-J, Baek S, Lee Y-J, Cho A, Mun J-H (2019) The radish genome database (RadishGD): an integrated information resource for radish genomics. Database 2019:baz009.

Kim HT, Kim JS, Lee YM, Mun J-H, Kim J-H (2019) Molecular markers for phylogenetic applications derived from comparative plastome analysis of Prunus species. J Syst Evol 57: 15-22.

Baek S, Choi K, Kim G-B, Yu H-J, Cho A, Jang H, Kim C, Kim H-J, Chang KS, Kim J-H, Mun J-H (2018) Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries. Genome Biol 19: 127.

Mun J-H, Lee Y-J, Jeong Y-M, Joo S-H, Yu H-J (2018) Assembly of a radish core collection for evaluation and preservation of genetic diversity. Hort Environ Biotechnol, 59:711-721.

Lim CE, Kim G-B, Ryu S-R, Yu H-J, Mun J-H (2018) The complete chloroplast genome of Artemisia hallaisanensis Nakai (Asteraceae), an endemic medicinal herb in Korea. Mitochondrial DNA Part B: Resources 3: 359-360.

Cho A, Baek S, Kim G-B, Shin C-H, Kim C-S, Choi K, Kang Y, Yu H-J, Kim J-H, Mun J-H (2017) Genomic clues to the parental origin of the wild flowering cherry Prunus yedoensis var. nudiflora (Rosaceae). Plant Biotechnol Rep 11:449–459.

Kwon Y-E, Yu H-J, Baek S, Kim G-B, Lim K-B, Mun J-H (2017) Development of gene-based identification markers for Phalaenopsis ‘KS Little Gem’ based on comparative genome analysis. Hortic Environ Biotechnol 58:162-169.

Yu H-H, Jeong Y-M, Mun J-H (2017) Comparative analysis of the radish genome with Brassica genomes. In: Takeshi Nishio and Hiroyasu Kitashiba (eds.) 2017. The Radish Genome, Springer Nature, Cham, Switzerland (ISBN 978-3-319-59252-7).

Lim CE, Kim G-B, Baek S, Han S-M, Yu H-J, Mun J-H (2016) The complete chloroplast genome of Aconitum chiisanense Nakai (Ranunculaceae) Mitochondrial DNA Part A 28: 75-76.

Kim N, Jeong YM, Jeong S, Kim GB, Baek S, Kwon YE, Cho A, Choi SB, Kim J, Lim WJ, Kim KH, Park W, Kim JY, Kim JH, Yim B, Lee YJ, Chun BM, Lee YP, Park BS, Yu H-J, Mun J-H (2016) Identification of candidate domestication regions in the radish genome based on high depth resequencing analysis of 17 genotypes. Theor Appl Genet 129: 1797-1814.

Jeong Y-M, Kim N, Ahn BO, Oh M, Chung WH, Chung H, Jeong S, Lim KB, Hwang YJ, Kim GB, Baek S, Choi SB, Hyung DJ, Lee SW, Sohn SH, Kwon SJ, Jin M, Seol YJ, Chae WB, Choi KJ, Park BS, Yu H-J, Mun J-H (2016) Elucidating the triplicated ancestral genome structure of radish based on chromosome level comparison with the Brassica genomes. Theor Appl Genet 129: 1357-1372.

Jeong Y-M, Chung W-H, Choi AY, Mun J-H, Kim N, Yu H-J. (2016) The complete mitochondria genome of cultivated radish WK10039 (Raphanus sativus L.) Mitochondrial DNA 27: 941-942.

Kim G-B, Kwon Y, Yu H-J, Lim K-B, Seo J-H, Mun J-H. (2016) The complete chloroplast genome of Phalaenopsis “Tiny Star”. Mitochondrial DNA 27: 1300-1302.

Larrainzar E, Riely BK, Kim SC, Carrasquilla-Garcia N, Yu H-J, Hwang HJ, Oh M, Kim GB, Surendrarao AK, Chasman D, Siahpirani AF, Penmetsa RV, Lee GS, Kim N, Roy S, Mun J-H, Cook DR (2015) Deep sequencing of the Medicago truncatula root transcriptome reveals a massive and early interaction between nodulation factor and ethylene signals. Plant Physiol 169: 233-265.

Yim B, Mun J-H, Jeong Y-M, Hur YY, Yu H-J (2015) Flower and microspore development in ‘Campbell Early’ (Vitis labruscana) and ‘Tamnara’ (V. spp.) grapes. Kor J Hort Sci Technol 33: 420-428.

Vo TC, Mun J-H, Yu H-J, Hwang Y-J, Chung M-Y, Kim C-K, Kim HY, Lim K-B (2015) Phenotypic analysis of parents and their reciprocal F1 hybrids in Phalaenopsis. Hort Environ Biotechnol 56: 612-617.

Mun J-H, Chung H, Chung W-H, Oh M, Jeong Y-M, Kim N, Ahn BO, Park B-S, Park S, Lim K-B, Hwang Y-J, Yu H-J (2015) Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing. Theor Appl Genet 128: 259-272.

Mun J-H, Yu H-J, Park B-S (2015) Genomic resources and physical mapping of the B. rapa genome. In: Xiaowu Wang and Chittaranjan Kole (eds.) 2015. The Brassica rapa Genome, Springer, Heidelberg, Germany (ISBN 978-3-662-47900-1).

Jeong Y-M, Chung W-H, Chung H, Kim N, Park B-S, Lim K-B, Yu H-J, Mun J-H (2014) Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica. Theor Appl Genet 127: 1975-1989.

Jeong Y-M, Chung W-H, Mun J-H, Kim N, Yu H-J (2014) De novo assembly and characterization of the complete chloroplast genome of radish (Raphanus sativus L.). Gene 551: 39-48.

Mun J-H, Chung H, Jeong YM, Lee SS, Chung WH, Yu HJ. (2014) Construction of a genetic map based on high-throughput SNP genotyping and genetic mapping of a TuMV resistance locus in Brassica rapa. Mol Genet Genomics 289: 149-160.

Laporte P, Lepage A, Fournier J, Catrice O, Moreau S, Jardinaud MF, Mun J-H, Larrainzar E, Cook DR, Gamas P, Niebel A. (2014) The CCAAT box-binding transcription factor NF-YA1 controls rhizobial infection. J Exp Bot 65: 481-494.

Riely B, Larrainzar E, Mun J-H, Gil-Quintana E, Gonzalez E, Haney C, Yu H-J, Tricoli D, Ehrhardt D, Long S, Cook D. (2013) Development of tools for the biochemical characterization of the symbiotic receptor-like kinase DMI2. Mol Plant Microbe Interact. 26: 216-226.

Seo MS, Jin M, Lee SS, Kwon SJ, Mun JH, Park BS, Visser RG, Bonnema G, Sohn SH. (2013) Mapping quantitative trait loci for tissue culture response in VCS3M-DH population of Brassica rapa. Plant Cell Rep 32:1251-1261.

Kim B, Yu H-J, Park S-G, Shin JY, Oh M, Kim N, Mun J-H (2012) Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing. BMC Plant Biol 12:218.

Mun J-H, Yu H-J, Shin JY, Oh M, Hwang H-J, Chung H (2012) Auxin response factor gene family in Brassica rapa: genomic organization, divergence, expression, and evolution. Mol Genet Genomics 287: 765-784.

Hwang Y-J, Yu H-J, Mun J-H, Ryu KB, Park B-S, Lim K-B (2012) Centromere repeat DNA originated from Brassica rapa is detected in the centromere region of Raphanus sativus chromosomes. Korean J Hort Sci & Technol 30: 751-756.

Yoon U-H, Lee J, Hahn J-H, Kim Y-K, Lee G-S, Ji H-S, Kim C-K, Mun J-H, Kim Y-M, Kim T-H (2012) Structural and expression analysis of prolamin genes in Oryza sativa L. Plant Biotechnol Rep 6: 251-262.

The Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43: 1035-1040 (Consortium Co-PI).

Young ND, Debellé F, Oldroyd G, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KFX, Gouzy J, Schoof S, de Peer YV, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, de Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KAT, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Doyle J, Dudez A-M, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray S, Jeong D-H, Jing Y, Jöcker A, Kenton SM, Kim D-J, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun J-H, Najar FZ, Nicholson C, Noirot C, O¡¯Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli D, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S,Sterck L, Viollet A, Wang B-B, Wang K, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao X, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA. (2011) The Medicago genome provides insight into evolution of rhizobial symbiosis. Nature 480: 520-524.

Wang X, Torres M, Pierce G, Lemke C, Nelson L, Yuksel B, Bowers J, Xiao Y, Lin L, Epps E, Sarazen H, Rogers C, Karunakaran S, Ingles J, Giattina E, Mun J-H, Seol Y-J, Park B-S, Amasino R, Quiros C, Osborn T, Pires JC, Town C, Paterson AH (2011) A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations. BMC Genomics 12: 470.

Park T-H, Park B-S Kim J-A, Hong J-K, Seol Y-J, Mun J-H (2011) Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project. J Genet Genomics 38: 47-53.

Yu H-J, Park S-G, Oh M, Hwang H-J, Kim N, Chung H, Sohn S-H, Park B-S, Mun J-H (2011) The Brassica rapa tissue-specific EST database. Kor J Hort Sci Technol 29: 633-640.

Mun J-H, Chung H, Lee S-C, Yu H-J (2011). Pickprimer: A graphic user interface program for primer design on the gene target region. Kor J Hort Sci Technol 29: 461-466.

Yoon U-H, Kim C-K, Lee G-S, Hahn J-H, Lee J, Kim Y-K, Ji H-S, Mun J-H, Lee T-H, Kim T-H (2011) Structural and expression analysis of glutelin genes in Oryza sativa L. J Plant Biotechnol 38: 176-185.

Park T-H, Jin M, Lee S-C, Hong JK, Seol Y-J, Mun J-H, Park B-S (2011) Tau class glutathione S-transferase candidates from Brassica rapa: genetic mapping and sequence analysis. Hort Environ Biotechnol 52: 284-291.

Mun J-H, Kwon S-J, Seol Y-J, Kim JA, Jin M, Kim JS, Lim M-H, Lee S-I, Hong JK, Park T-H, Lee S-C, Kim B-J, Seo M-S, Baek S, Lee M-J, Shin JY, Hahn J-H, Hwang Y-J, Lim K-B, Park JY, Lee J, Yang T-J, Yu H-J, Choi I-Y, Choi B-S, Choi SR, Ramchiary N, Lim YP, Fraser F, Drou N, Soumpourou E, Trick M, Bancroft I, Shrpe AG, Parkin IAP, Batley J, Edwards D, Park B-S (2010) Sequence and structure of Brassica rapa chromosome A3. Genome Biology 11: R94.

Mun J-H, Yang T-J, Kwon S-J, Park B-S (2011) Brassica rapa genome sequencing project-strategies and current status. In: Jan Sadowski (ed.) 2011. Genetics, genomics and breeding of vegetable Brassicas. Science Publishers, Enfield, USA (ISBN 978-1-5780-8706-8).

Mun J-H, Park B-S. (2011) Sequencing the gene space of Brassica rapa. In: Ian Bancroft (ed.) 2011. Genetics and Genomics of the Brassicaceae, Springer, New York, USA (ISBN 978-1-4419-7117-3).

Park S, Yu H-J, Mun J-H, Lee S-C (2010) Genome-wide discovery of DNA polymorphism in Brassica rapa. Mol Gen Genomics 283: 135-145.

Mun J-H, Kwon S-J, Park B-S (2010) The strategy and current status of Brassica rapa genome project. J Plant Biotechnol 37: 153-165.

Mun J-H, Kwon S-J, Yang T-J, Seol Y-J, Jin M, Kim J-A, Lim M-H, Kim JS, Baek S, Choi B-S, Yu H-J, Kim D-S, Kim N, Lim K-B, Lee S-I, Hahn J-H, Lim YP, Bancroft I, Park B-S (2009) Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol 10: R111.

Mun J-H, Yu H-J, Park S, Park B-S (2009) Genome-wide identification of NBS-encoding resistance genes in Brassica rapa. Mol Genet Genomics 282: 617-631.

Trick M, Kwon S-J, Choi SR, Fraser F, Soumpourou E, Wang Z, Lee SY, Yang T-J, Mun J-H, Paterson AH, Town CD, Pires JC, Lim YP, Park B-S, Bancroft I (2009) Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence level analysis. BMC Genomics 10: 539.

Zang Y-X, Kim HU, Kim J, Lim M-H, Jin M, Lee SC, Kwon S-J, Lee SI, Hong JK, Park T-H, Mun J-H, Seol Y-J, Hong S-B, Park B-S (2009) Genome-wide identification of glucosinolate synthesis genes in Brassica rapa. FEBS J 276: 3559-3574.

Hong JK, Hwang JE, Park T-H, Zang Y-X, Lee SC, Kwon S-J, Mun J-H, Kim HU, Kim JA, Jin M, Kim JS, Lee SI, Lim M-H, Her Y, Lim CO, Park B-S (2008) Identification and characterization of the phytocystatin family from Brassica rapa. J Plant Biotechnol 35: 317-327.

Mun J-H, Kwon S-J, Yang T-J, Kim H-S, Choi B-S, Baek S, Kim JS, Jin M, Kim J-A, Lim M-H, Lee SI, Kim H-I, Kim H, Lim YP, Park B-S (2008) The first generation of BAC-based physical map of Brassica rapa. BMC Genomics 9: 280.

Lee S-C, Lim M-H, Kim J-A, Lee S-I, Kim J-S, Jin M, Kwon S-J, Mun J-H, Kim Y-K, Kim H-U, Hur Y, Park B-S (2008) Transcriptome analysis in Brassica rapa under the abiotic stresses using Brassica 24K oligo microarray. Mol Cells 26: 595-605.

Mun J-H, Messinese E, Yeun LH, Jayaraman D, Rougé P, Barre A, Lougnon G, Schornack S, Bono J-J, Cook DR, Ané J-M (2007) A novel nuclear protein interacts with the symbiotic DMI3 CCaMK in Medicago truncatula. Mol Plant Microbe Interact 20: 912-921.

Jeong Y-M, Mun J-H, Kim H, Lee S-Y, Kim S-G (2007) An upstream region in the first intron of petunia actin-depolymerizing factor 1 alters tissue-specific expression in transgenic Arabidopsis (Arabidopsis thaliana). Plant J 50: 230-239.

Mun J-H, Kim D-J, Choi H-K, Gish J, Debelle F, Mudge J, Denny R, Endre G, Saurat O, Dudez A-M, Kiss GB, Roe B, Young ND, Cook DR (2006) Distribution of microsatellites in the genome of Medicago truncatula: A resource of genetic markers that integrate genetic and physical maps. Genetics 172: 2541-2555.

Riely BK, Mun J-H, Ané J-M (2006) Unravelling the molecular basis for symbiotic signal transduction in legumes. Mol Plant Pathol 7: 197-207.

Jeong Y-M, Mun J-H, Lee I, Woo JC, Hong CB, Kim S-G (2006) Distinct roles of the first introns on the expression of Arabidopsis profilin gene family members. Plant Physiol 140: 196-209.

Mun J-H, Choi H-K, Kim D-J, Zhu H, Baek J-M, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci 101: 15289-15294.

Choi H-K, Kim D-J, Uhm T, Limpens E, Lim H, Mun J-H, Kalo P, Penmetsa RV, Seres, Kulikova AO, Roe BA, Bisseling T, KissGB, Cook DR (2004) A sequence-based genetic map of Medicago truncatula and comparison of marker co-linearity with Medicago sativa. Genetics 166: 1463-1502.

Mun J-H, Lee S-Y, Yu H-J, Jeong Y-M, Shin M-Y, Kim H, Lee I, Kim S-G (2002) Petunia actin-depolymerizing factors are mainly accumulated in vascular tissue and their expressions are enhanced by the first intron. Gene 292: 233-243.

Kim H, Mun J-H, Byun BH, Hwang H-J, Kwon YM, Kim S-G (2002) Molecular cloning and characterization of the gene encoding osmotin protein in Petunia hybrid. Plant Science 162:745-752.

Mun J-H, Yu H-J, Lee HS, Kwon YM, Lee JS, Lee I, Kim S-G (2000) Two closely related cDNAs encoding actin-depolymerizing factors of petunia are mainly expressed in vegetative tissues. Gene 257: 167-176.

Lee HS, Mun J-H, Kwon YM, Lee JS, Kim S-G (1999) Characterization of cDNAs encoding cytoplasmic ribosomal protein L15 and L27a in petunia (Petunia hybrida): Primary structures and coordinate expression. Gene 226: 155-163.

Yu H-J, Moon MS, Lee HS, Mun J-H, Kwon YM, Kim S-G (1999) Analysis of cDNAs expressed during first cell division of petunia petal protoplast cultures using expressed sequence tags. Mol Cells 9: 258-264.

Yu H-J, Mun J-H, Kwon YM, Lee JS, Kim S-G (1999) Two cDNAs encoding pathogenesis-related proteins of Lithospermum erythrorhizon display different expression patterns in suspension cultures. J Plant Physiol 155: 364-370.

Mun J-H, Park C-W (1995) Flavonoid chemistry of Polygonum sect Tovara (Polygonaceae): a systematic survey. Pl Syst Evol 196: 153-159.