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Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes

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This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome.

Abstract

Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

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References

  • Al-Shehbaz I (1984) The tribes of Cruciferae (Brassicaceae) in the southeastern United States. J Arnold Arbor Harv Univ 65:343–373

    Google Scholar 

  • American Society of Agronomy (2009) Radishes: a new cover crop option. Crops and soils. American Society of Agronomy, Madison, pp 14–17

    Google Scholar 

  • Arias T, Pires J (2012) A fully resolved chloroplast phylogeny of the brassica crops and wild relatives (Brassicaceae: Brassiceae): novel clades and potential taxonomic implications. Taxon 61:980–988

    Google Scholar 

  • Arumugam N, Mukhopadhyay A, Gupta V, Sodhi Y, Verma J, Pental D, Pradhan A (2002) Synthesis of somatic hybrids (RCBB) by fusing heat-tolerant Raphanus sativus (RR) and Brassica oleracea (CC) with Brassica nigra (BB). Plant Breed 121:168–170

    Article  Google Scholar 

  • Beilstein M, Al-Shehbaz I, Kellogg E (2006) Brassicaceae phylogeny and trichome evolution. Am J Bot 93:607–619

    Article  CAS  PubMed  Google Scholar 

  • Chang S, Yang T, Du T, Huang Y, Chen J, Yan J, He J, Guan R (2011) Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica. BMC Genom 12:497

    Article  CAS  Google Scholar 

  • Cheng F, Mandáková T, Wu J, Xie Q, Lysak M, Wang X (2013a) Deciphering the diploid ancestral genome of the mesohexaploid Brassica rapa. Plant Cell 25:1541–1554

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng F, Wu J, Fang L, Sun S, Liu B, Lin K, Bonnema G, Wang X (2013b) Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS ONE 7:e36442

    Article  Google Scholar 

  • Cheng F, Wu J, Wang X (2014) Genome triplication drove the diversification of Brassica plants. Hort Res 1:14024

    Article  Google Scholar 

  • Edgar R (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fischer S, Brunk B, Chen F, Gao X, Harb O, Iodice JB, Shanmugam D, Roos D, Stoeckert CJ (2011) Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics 35:6.12.11–16.12.19

  • Haas B, Salzberg S, Zhu W, Pertea M, Allen J, Orvis J, White O, Buell C, Wortman J (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol 9:R7

    Article  PubMed  PubMed Central  Google Scholar 

  • Hall A, Fiebig A, Preuss D (2002) Beyond the Arabidopsis genome: opportunities for comparative genomics. Plant Physiol 129:1439–1447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hegde SG, Nason JD, Clegg JM, Ellstrand NC (2006) The evolution of California’s wild radish has resulted in the extinction of its progenitors. Evolution 60:1187–1197

    Article  PubMed  Google Scholar 

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

    CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Johnston J, Pepper A, Hall A, Chen Z, Hodnett G, Drabek J, Lopez R, Price H (2005) Evolution of genome size in Brassicaceae. Ann Bot 95:229–253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaneko Y, Kimizuka-Takagi C, Bang S, Matsuzawa Y (2007) Radish. In: Kole C (ed) Vegetables. Springer, Berlin Heidelberg, pp 141–160

    Chapter  Google Scholar 

  • Kim B, Yu H-J, Park S-G, Shin J, 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kitashiba H, Li F, Hirakawa H, Kawanabe T, Zou Z, Hasegawa Y, Tonosaki K, Shirasawa S, Fukushima A, Yokoi S, Takahata Y, Kakizaki T, Ishida M, Okamoto S, Sakamoto K, Shirasawa K, Tabata S, Nishio T (2014) Draft sequences of the radish (Raphanus sativus L.) genome. DNA Res 21:481–490

    Article  PubMed  PubMed Central  Google Scholar 

  • Koch M, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17:1483–1498

    Article  CAS  PubMed  Google Scholar 

  • Kopta T, Pokluda R (2013) Yields, quality and nutritional parameters of radish (Raphanus sativus) cultivars when grown in organically in Czech Republic. Hort Sci 40:16–21

    CAS  Google Scholar 

  • Korf I (2004) Gene finding in novel genomes. BMC Bioinformatics 5:59

    Article  PubMed  PubMed Central  Google Scholar 

  • Kuepper G, Dodson M (2001) Companion planting: basic concepts and resources. NCAT National Center for Appropriate Technology, Butte

    Google Scholar 

  • Lee S-S, Lee S-A, Yang J, Kim J (2011) Developing stable progenies of xBrassicoraphanus, an intergeneric allopolyploid between Brassica rapa and Raphanus sativus, through induced mutation using microspore culture. Theor Appl Genet 122:885–891

    Article  PubMed  Google Scholar 

  • Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder O, Leung F, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner C, Lam T, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford M, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam T, Yiu S, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong G, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J (2010) The sequence and de novo assembly of the giant panda genome. Nature 463:311–317

    Article  CAS  PubMed  Google Scholar 

  • Li F, Hasegawa Y, Saito M, Shirasawa S, Fukushima A, Ito T, Fujii H, Kishitani S, Kitashiba H, Nishio T (2011) Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.). DNA Res 18:401–411

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Linnaeus C (1753) Species Plantarum. L. Salvius, Stockholm

  • Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin I, Zhao M, Ma J, Yu J, Huang S, Wang X, Wang J, Lu K, Fang Z, Bancroft I, Yang T, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King G, Pires J, Lu C, Wu Z, Sampath P, Wang Z, Guo H, Pan S, Yang L, Min J, Zhang D, Jin D, Li W, Belcram H, Tu J, Guan M, Qi C, Du D, Li J, Jiang L, Batley J, Sharpe A, Park B, Ruperao P, Cheng F, Waminal N, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee T, Wang J, Jin H, Li Z, Li X, Zhang J, Xiao L, Zhou Y, Liu Z, Liu X, Qin R, Tang X, Liu W, Wang Y, Zhang Y, Lee J, Kim H, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson A (2014) The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun 5:3930

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lowe T, Eddy S (1997) tRNAscan-SE: a program for inproved detection of transfer RNA genes in genomic sequence. Nucleic Acid Res 25:955–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu N, Yamane K, Ohnishi O (2008) Genetic diversity of cultivated and wild radish and phylogenetic relationships among Raphanus and Brassica species revealed by the analysis of trnK/matK sequence. Breed Sci 58:15–22

    Article  CAS  Google Scholar 

  • Lysak M, Cheung K, Kitschke M, Bures P (2007) Ancestral chromosomal blocks are triplicated in Brassiceae species with varying chromosome number and genome size. Plant Physiol 145:402–410

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marçais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764–770

    Article  PubMed  PubMed Central  Google Scholar 

  • Matsuzawa Y, Sarashima M (1986) Intergeneric hybridization between Raphanus sativus L. and Brassica nigra Koch. and alloplasmic radish derivative. Breed Sci 36:122–130

    Google Scholar 

  • Mitsui Y, Shimomura M, Komatsu K, Namiki N, Shibata-Hatta M, Imai M, Katayose Y, Mukai Y, Kanamori H, Kurita K, Kagami T, Wakatsuki A, Ohyanagi H, Ikawa H, Minaka N, Nakagawa K, Shiwa Y, Sasaki T (2015) The radish genome and comprehensive gene expression profile of tuberous root formation and development. Sci Rep 5:10835

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moghe G, Hufnagel D, Tang H, Xiao Y, Dworkin I, Town C, Conner J, Shiu S (2014) Consequences of whole-genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species. Plant Cell 26:1925–1937

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mun J-H, Kwon SJ, Yang TJ, Seol YJ, Jin M, Kim JA, Lim MH, Kim JS, Lee SI, Baek S, Choi BS, Kim DS, Kim N, Yu HJ, Lim KB, Lim YP, Bancroft I, Hahn JH, Park BS (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

    Article  PubMed  PubMed Central  Google Scholar 

  • Mun J-H, Kwon S, Seol Y, Kim J, Jin M, Kim J, Lim M, Lee S, Hong J, Park T, Lee S, Kim B, Seo M, Baek S, Lee M, Shin J, Hahn J, Hwang Y, Lim K, Park J, Lee J, Yang T, Yu H-J, Choi I, Choi B, Choi S, Ramchiary N, Lim Y, Fraser F, Drou N, Soumpourou E, Trick M, Bancroft I, Sharpe A, Parkin I, Batley J, Edwards D, Park B (2010) Sequence and structure of Brassica rapa chromosome A3. Genome Biol 11:R94

    Article  PubMed  PubMed Central  Google Scholar 

  • Mun J-H, Chung H, Chung W-H, Oh M, Jeong Y-M, Kim N, Ahn B, 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

    Article  CAS  PubMed  Google Scholar 

  • U N (1935) Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn J Bot 7:389–452

    Google Scholar 

  • Nagpal R, Dar T, Raina S (2008) Molecular systematics of Brassica and allied genera in subtribes Brassicinae, Raphaninae, Moricandiinae, and Cakilinae (Brassicaceae, tribe Brassiceae); the organization and evolution of ribosomal gene families. Bot J Linn Soc 157:545–557

    Article  Google Scholar 

  • Navabi Z-K, Huebert T, Sharpe A, O’Neill C, Bancroft I, Parkin IA (2013) Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea. BMC Genom 14:250

    Article  CAS  Google Scholar 

  • Nelson M, Parkin I, Lydiate D (2011) The mosaic of ancestral karyotype blocks in the Sinapis alba L. genome. Genome 54:33–41

    Article  CAS  PubMed  Google Scholar 

  • Nussbaumer T, Martis M, Roessner S, Pfeifer M, Bader K, Sharma S, Gundlach H, Spannagl M (2013) MIPS PlantsDB: a database framework for comparative plant genome research. Nucleic Acids Res 41:D1144–D1151

    Article  CAS  PubMed  Google Scholar 

  • Ossowski S, Schneeberger K, Lucas-Lledó J, Warthmann N, Clark R, Shaw R, Weigel D, Lynch M (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:92–94

    Article  CAS  PubMed  Google Scholar 

  • Panjabi P, Jagannath A, Bisht N, Padmaja K, Sharma S, Gupta V, Pradhan A, Pental D (2008) Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genom 9:113

    Article  Google Scholar 

  • Paritosh K, Gupta V, Yadava S, Singh P, Pradhan A, Pental D (2014) RNA-seq based SNPs for mapping in Brassica juncea (AABB): synteny analysis between the two constituent genomes A (from B. rapa) and B (from B. nigra) shows highly divergent gene block arrangement and unique block fragmentation patterns. BMC Genom 15:396

    Article  Google Scholar 

  • Prakash S, Bhat S, Quiros C, Kirti P, Chopra V (2009) Brassica and its close allies: cytogenetics and evolution. In: Jules J (ed) Plant breed reviews, vol 31. Wiley, London, pp 21–187

    Chapter  Google Scholar 

  • Schranz ME, Lysak MA, Mitchell-Olds T (2006) The ABC’s of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Trends Plant Sci 11:535–542

    Article  CAS  PubMed  Google Scholar 

  • Shen D, Sun HH, Huang MY, Zheng Y, Li XX, Fei ZJ (2013) RadishBase: a database for genomics and genetics of radish. Plant Cell Physiol 54:e3

    Article  CAS  PubMed  Google Scholar 

  • Song K, Osborn T, Williams P (1988) Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs): 2. Preliminary analysis of subspecies within B. rapa (syn. campestris) and B. oleracea. Theor Appl Genet 76:593–600

    Article  CAS  PubMed  Google Scholar 

  • Song K, Osborn T, Williams P (1990) Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs): 3. Genomic relationships in Brassica and related genera and the origin of B. oleracea and B. rapa (syn. campestris). Theor Appl Genet 79:497–506

    Article  CAS  PubMed  Google Scholar 

  • Stanke M, Morgenstern B (2005) AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acid Res 33:W465–W467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Thormann CE, Ferreira ME, Camargo LE, Tivang JG, Osborn TC (1994) Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species. Theor Appl Genet 88:973–980

    Article  CAS  PubMed  Google Scholar 

  • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D, Pimentel H, Salzberg S, Rinn J, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang S, Wang X, He Q, Liu X, Xu W, Li L, Gao J, Wang F (2012a) Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep 31:1437–1447

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Tang H, DeBarry J, Tan X, Li J, Wang X, Lee T, Jin H, Marler B, Guo H, Kissinger J, Paterson A (2012b) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40:e49

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Pan Y, Liu Z, Zhu X, Zhai L, Xu L, Yu R, Gong Y, Liu L (2013a) De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism. BMC Genom 14(1):836

    Article  CAS  Google Scholar 

  • Wang Y, Xu L, Chen Y, Shen H, Gong Y, Limera C, Liu L (2013b) Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to lead (Pb) stress with next generation sequencing. PLoS ONE 8:e66539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Warwick S, Al-Shehbaz I (2006) Brassicaceae: chromosome number index and database on CD-Rom. Pl Syst Evol 259:237–248

    Article  Google Scholar 

  • Warwick S, Black L (1991) Molecular systematics of Brassica and allied genera (Subtribe Brassicinae, Brassiceae)—chloroplast genome and cytodeme congruence. Theor Appl Genet 82:81–92

    Article  CAS  PubMed  Google Scholar 

  • Warwick S, Black L (1994) Evaluation of the subtribes Moricandiinae, Savignyinae, Vellinae and Zillinae (Brassicaceae, tribe Brassiceae) using chloroplast DNA restriction site variation. Can J Bot 72:1692–1701

    Article  Google Scholar 

  • Warwick S, Black L (1997) Phylogenetic implications of chloroplast DNA restriction site variation in subtribes Raphaninae and Cakilinae (Brassicaceae, tribe Brassiceae). Can J Bot 75:960–973

    Article  Google Scholar 

  • Warwick S, Sauder C (2005) Phylogeny of tribe Brassiceae (Brassicaceae) based on chloroplast restriction site polymorphisms and nuclear ribosomal internal transcribed spacer and chloroplast trnL intron sequences. Can J Bot 83:467–483

    Article  CAS  Google Scholar 

  • Wu T, Nacu N (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26:873–881

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie Y, Ye S, Wang Y, Xu L, Zhu X, Yang J, Feng H, Yu R, Karanja B, Gong Y, Liu L (2015) Transcriptome-based gene profiling provides novel insights into the characteristics of radish root response to Cr stress with next-generation sequencing. Front Plant Sci 6:202

    PubMed  PubMed Central  Google Scholar 

  • Yamagishi H, Tanaka Y, Terachi T (2014) Complete mitochondrial genome sequence of black mustard (Brassica nigra; BB) and comparison with Brassica oleracea (CC) and Brassica carinata (BBCC). Genome 57:577–582

    Article  CAS  PubMed  Google Scholar 

  • Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591

    Article  CAS  PubMed  Google Scholar 

  • Yang YW, Tseng PF, Tai PY, Chang CJ (1998) Phylogenetic position of Raphanus in relation to Brassica species based on 5S rRNA spacer sequence data. Bot Bull Acad Sin 39:153–160

    CAS  Google Scholar 

  • Yang YW, Lai KN, Tai PY, Ma DP, Li WH (1999) Molecular phylogenetic studies of Brassica, Rorippa, Arabidopsis and allied genera based on the internal transcribed spacer region of 18S-25S rDNA. Mol Phylogenet Evol 13:455–462

    Article  CAS  PubMed  Google Scholar 

  • Yang Y, Tai P, Chen Y, Li W (2002) A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA. Mol Phylogenet Evol 23:268–275

    Article  CAS  PubMed  Google Scholar 

  • Zhang H, Meltzer P, Davis S (2013) RCircos: ans R package for Circos 2D track plots. BMC Bioinformatics 14:244

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported by Grants from the Next-Generation Biogreen21 program (PJ01108601 to JHM, PJ01108602 to HJY, and PJ008019 to BOA, NK, and HJY) and the National Academy of Agricultural Science (PJ009795 to JHM), Rural Development Administration, Korea.

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    Authors and Affiliations

    1. Department of Life Science, The Catholic University of Korea, Bucheon, 420-743, Korea

      Young-Min Jeong, Hee Chung & Hee-Ju Yu

    2. Epigenomics Research Center of Genome Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea

      Namshin Kim & Seongmun Jeong

    3. Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Korea

      Byung Ohg Ahn, Mijin Oh, Seong-Han Sohn, Soo-Jin Kwon, Mina Jin, Young-Joo Seol & Beom-Seok Park

    4. Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea

      Won-Hyong Chung

    5. Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Korea

      Ki-Byung Lim

    6. Department of Life Science, Sahmyook University, Seoul, 139-800, Korea

      Yoon-Jung Hwang

    7. Department of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea

      Goon-Bo Kim, Seunghoon Baek, Sang-Bong Choi & Jeong-Hwan Mun

    8. SeqGenesis, Daejeon, 305-343, Korea

      Dae-Jin Hyung & Seung-Won Lee

    9. Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 565-852, Korea

      Won Byoung Chae & Keun Jin Choi

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    1. Young-Min Jeong
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    Correspondence to Hee-Ju Yu or Jeong-Hwan Mun.

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    The authors declare that the experiments complied with current laws of the country in which they were performed.

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    The authors declare that they have no conflict of interest.

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    Communicated by I. Parkin.

    Y. -M. Jeong, N. Kim and B. O. Ahn contributed equally to this work.

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    Jeong, YM., Kim, N., Ahn, B.O. et al. Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes. Theor Appl Genet 129, 1357–1372 (2016). https://doi.org/10.1007/s00122-016-2708-0

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    • DOI: https://doi.org/10.1007/s00122-016-2708-0

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