[KSCI] Korea Science Citation Index Service

http://dx.doi.org/10.1016/j.jgr.2013.12.005

Evidence of genome duplication revealed by sequence analysis of multi-loci expressed sequence tagesimple sequence repeat bands in Panax ginseng Meyer

Kim, Nam-Hoon (Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Choi, Hong-Il (Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Kim, Kyung Hee (Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Jang, Woojong (Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Yang, Tae-Jin (Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)

Publication Information

Journal of Ginseng Research / v.38, no.2, 2014 , pp. 130-135 More about this Journal

Abstract

Background: Panax ginseng, the most famous medicinal herb, has a highly duplicated genome structure. However, the genome duplication of P. ginseng has not been characterized at the sequence level. Multiple band patterns have been consistently observed during the development of DNA markers using unique sequences in P. ginseng. Methods: We compared the sequences of multiple bands derived from unique expressed sequence tagsimple sequence repeat (EST-SSR) markers to investigate the sequence level genome duplication. Results: Reamplification and sequencing of the individual bands revealed that, for each marker, two bands around the expected size were genuine amplicons derived from two paralogous loci. In each case, one of the two bands was polymorphic, showing different allelic forms among nine ginseng cultivars, whereas the other band was usually monomorphic. Sequences derived from the two loci showed a high similarity, including the same primer-binding site, but each locus could be distinguished based on SSR number variations and additional single nucleotide polymorphisms (SNPs) or InDels. A locus-specific marker designed from the SNP site between the paralogous loci produced a single band that also showed clear polymorphism among ginseng cultivars. Conclusion: Our data imply that the recent genome duplication has resulted in two highly similar paralogous regions in the ginseng genome. The two paralogous sequences could be differentiated by large SSR number variations and one or two additional SNPs or InDels in every 100 bp of genic region, which can serve as a reliable identifier for each locus.

Keywords

genome duplication; multi-band pattern; Panax ginseng; paralogs; SSR marker;

Citations & Related Records

Times Cited By KSCI : 4 (Citation Analysis)

Reference
Cited By KSCI

1	Kim J, Jo BH, Lee KL, Yoon ES, Ryu GH, Chung KW. Identification of new microsatellite markers in Panax ginseng. Mol Cell 2007;24:60-8.
2	Ma KH, Dixit A, Kim YC, Lee DY, Kim TS, Cho EG, Park YJ. Development and characterization of new microsatellite markers for ginseng (Panax ginseng C.A. Meyer). Conserv Genet 2007;8:1507-9. DOI ScienceOn
3	Dan NV, Ramchiary N, Choi SR, Uhm TS, Yang TJ, Ahn IO, Lim YP. Development and characterization of new microsatellite markers in Panax ginseng (C.A. Meyer) from BAC end sequences. Conserv Genet 2010;11:1223-5. DOI ScienceOn
4	Kim JH, Jung JY, Choi HI, Kim NH, Park JY, Lee Y, Yang TJ. Diversity and evolution of major Panax species revealed by scanning the entire chloroplast intergenic spacer sequences. Genet Resour Crop Evol 2013;60:413-25. DOI
5	Allen GC, Flores-Vergara MA, Krasnyanski S, Kumar S, Thompson WF. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat Protoc 2006;1:2320-5. DOI ScienceOn
6	Kumar S, Nei M, Dudley J, Tamura K. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 2008;9: 299-306. DOI ScienceOn
7	Kwok S, Kellogg DE, McKinney N, Spasic D, Goda L, Levenson C, Sninsky JJ. Effects of primer template mismatches on the polymerase chain-reactiondhuman- immunodeficiency-virus type-1 model studies. Nucleic Acids Res 1990;18:999-1005. DOI ScienceOn
8	Blanc G,Wolfe KH.Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 2004;16:1667-78. DOI ScienceOn
9	Sanzol J. Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data. BMC Plant Biol 2010;10:87. DOI ScienceOn
10	Choi HI, Kim NH, Jung JY, Park HM, Park HS, Park JY, Lee JH, Park JS, Lee JK, Choi BS, et al. Current status of Korean ginseng (Panax ginseng) genome mapping and sequencing. In: Yang DC, Kim SK, Oh HI, editors. Advances in ginseng researchdproceedings of the 10th international symposium on ginseng: September 13-16. Seoul, Korea: The Korean Society of Ginseng; 2010. pp. 762-78.
11	Yang TJ, Kim JS, Kwon SJ, Lim KB, Choi BS, Kim JA, Jin M, Park JY, Lim MH, Kim HI, et al. Sequence-level analysis of the diploidization process in the triplicated Flowering Locus C region of Brassica rapa. Plant Cell 2006;18: 1339-47. DOI ScienceOn
12	Choi HI, Kim NH, Lee JK, Choi BS, Kim KD, Park JY, Lee SC, Yang TJ. Evolutionary relationship of Panax ginseng and P. quinquefolius inferred from sequencing and comparative analysis of expressed sequence tags. Genet Resour Crop Evol 2013;60:1377-87. DOI
13	Choi HK, Wen J. A phylogenetic analysis of Panax (Araliaceae): integrating cpDNA restriction site and nuclear rDNA ITS sequence data. Plant Syst Evol 2000;224:109-20. DOI
14	Choi HW, Koo DH, Bang KH, Paek KY, Seong NS, Bang JW. FISH and GISH analysis of the genomic relationships among Panax species. Genes Genomics 2009;31:99-105. DOI ScienceOn
15	Doyle JJ, Egan AN. Dating the origins of polyploidy events. New Phytol 2010;186:73-85. DOI
16	Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science 2000;290:1151-5. DOI ScienceOn
17	Choi HI, Kim NH, Kim JH, Choi BS, Ahn IO, Lee JS, Yang TJ. Development of reproducible EST-derived SSR markers and assessment of genetic diversity in Panax ginseng cultivars and related species. J Ginseng Res 2011;35:399-412. DOI ScienceOn
18	Kim NH, Choi HI, Ahn IO, Yang TJ. EST-SSR marker sets for practical authentication of all nine registered ginseng cultivars in Korea. J Ginseng Res 2012;36:298-307. DOI ScienceOn
19	Lee JS, Lee SS, Lee JH, Ahn IO. Effect of seed size and cultivars on the ratio of seed coat dehiscence and seedling performance in Panax ginseng. J Ginseng Res 2008;32:257-63. DOI ScienceOn
20	Walsh PS, Fildes NJ, Reynolds R. Sequence analysis and characterization of stutter products at the tetranucleotide repeat locus vWA. Nucleic Acids Res 1996;24:2807-12. DOI
21	Bovo D, Rugge M, Shiao YH. Origin of spurious multiple bands in the amplification of microsatellite sequences. Mol Pathol 1999;52:50-1. DOI
22	Hong CP, Lee SJ, Park JY, Plaha P, Park YS, Lee YK, Choi JE, Kim KY, Lee JH, Lee J, et al. Construction of a BAC library of Korean ginseng and initial analysis of BAC-end sequences. Mol Genet Genomics 2004;271:709-16.
23	Wells R, Trick M, Fraser F, Soumpourou E, Clissold L, Morgan C, Pauquet J, Bancroft I. Sequencing-based variant detection in the polyploid crop oilseed rape. BMC Plant Biol 2013;13:111. DOI
24	Bowers JE, Chapman BA, Rong JK, Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003;422:433-8. DOI ScienceOn
25	Yun TK. Brief introduction of Panax ginseng C.A. Meyer. J Korean Med Sci 2001;16:S3-5. DOI
26	Waminal NE, Park HM, Ryu KB, Kim JH, Yang TJ, Kim HH. Karyotype analysis of Panax ginseng C.A.Meyer, 1843 (Araliaceae) based on rDNA loci and DAPI band distribution. Comp Cytogen 2012;6:425-41. DOI
27	Sterck L, Rombauts S, Jansson S, Sterky F, Rouzé P, Van de Peer Y. EST data suggest that poplar is an ancient polyploid. New Phytol 2005;167: 165-70. DOI ScienceOn
28	Fernando P, Evans BJ, Morales JC, Melnick DJ. Electrophoresis artefactsda previously unrecognized cause of error in microsatellite analysis. Mol Ecol Notes 2001;1:325-8. DOI

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