Evidence of genome duplication revealed by sequence analysis of multi-loci expressed sequence tag–simple sequence repea… (2024)

1. Next-Generation BioGreen21 Program
2. Rural Development Administration, Korea

1. Yun, Brief introduction of Panax ginseng C.A. Meyer, J Korean Med Sci, № 16, с. S3
   https://doi.org/10.3346/jkms.2001.16.S.S3
2. Hong, Construction of a BAC library of Korean ginseng and initial analysis of BAC-end sequences, Mol Genet Genomics, № 271, с. 709
   https://doi.org/10.1007/s00438-004-1021-9
3. Waminal, Karyotype analysis of Panax ginseng C.A.Meyer, 1843 (Araliaceae) based on rDNA loci and DAPI band distribution, Comp Cytogen, № 6, с. 425
   https://doi.org/10.3897/compcytogen.v6i4.3740
4. Choi, A phylogenetic analysis of Panax (Araliaceae): integrating cpDNA restriction site and nuclear rDNA ITS sequence data, Plant Syst Evol, № 224, с. 109
   https://doi.org/10.1007/BF00985269
5. Choi, FISH and GISH analysis of the genomic relationships among Panax species, Genes Genomics, № 31, с. 99
   https://doi.org/10.1007/BF03191143
6. Doyle, Dating the origins of polyploidy events, New Phytol, № 186, с. 73
   https://doi.org/10.1111/j.1469-8137.2009.03118.x
7. Choi, Evolutionary relationship of Panax ginseng and P. quinquefolius inferred from sequencing and comparative analysis of expressed sequence tags, Genet Resour Crop Evol, № 60, с. 1377
   https://doi.org/10.1007/s10722-012-9926-3
8. Lynch, The evolutionary fate and consequences of duplicate genes, Science, № 290, с. 1151
   https://doi.org/10.1126/science.290.5494.1151
9. Choi, Development of reproducible EST-derived SSR markers and assessment of genetic diversity in Panax ginseng cultivars and related species, J Ginseng Res, № 35, с. 399
   https://doi.org/10.5142/jgr.2011.35.4.399
10. Kim, EST-SSR marker sets for practical authentication of all nine registered ginseng cultivars in Korea, J Ginseng Res, № 36, с. 298
    https://doi.org/10.5142/jgr.2012.36.3.298
11. Kim, Identification of new microsatellite markers in Panax ginseng, Mol Cell, № 24, с. 60
    https://doi.org/10.1016/S1016-8478(23)10756-4
12. Ma, Development and characterization of new microsatellite markers for ginseng (Panax ginseng C.A. Meyer), Conserv Genet, № 8, с. 1507
    https://doi.org/10.1007/s10592-007-9284-4
13. Dan, Development and characterization of new microsatellite markers in Panax ginseng (C.A. Meyer) from BAC end sequences, Conserv Genet, № 11, с. 1223
    https://doi.org/10.1007/s10592-009-9924-y
14. Kim, Diversity and evolution of major Panax species revealed by scanning the entire chloroplast intergenic spacer sequences, Genet Resour Crop Evol, № 60, с. 413
    https://doi.org/10.1007/s10722-012-9844-4
15. Allen, A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide, Nat Protoc, № 1, с. 2320
    https://doi.org/10.1038/nprot.2006.384
16. Kumar, MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences, Brief Bioinform, № 9, с. 299
    https://doi.org/10.1093/bib/bbn017
17. Kwok, Effects of primer template mismatches on the polymerase chain-reaction—human-immunodeficiency-virus type-1 model studies, Nucleic Acids Res, № 18, с. 999
    https://doi.org/10.1093/nar/18.4.999
18. Blanc, Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes, Plant Cell, № 16, с. 1667
    https://doi.org/10.1105/tpc.021345
19. Sanzol, Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data, BMC Plant Biol, № 10, с. 87
    https://doi.org/10.1186/1471-2229-10-87
20. Sterck, EST data suggest that poplar is an ancient polyploid, New Phytol, № 167, с. 165
    https://doi.org/10.1111/j.1469-8137.2005.01378.x
21. Lee, Effect of seed size and cultivars on the ratio of seed coat dehiscence and seedling performance in Panax ginseng, J Ginseng Res, № 32, с. 257
    https://doi.org/10.5142/JGR.2008.32.3.257
22. Walsh, Sequence analysis and characterization of stutter products at the tetranucleotide repeat locus vWA, Nucleic Acids Res, № 24, с. 2807
    https://doi.org/10.1093/nar/24.14.2807
23. Fernando, Electrophoresis artefacts—a previously unrecognized cause of error in microsatellite analysis, Mol Ecol Notes, № 1, с. 325
    https://doi.org/10.1046/j.1471-8278.2001.00083.x
24. Bovo, Origin of spurious multiple bands in the amplification of microsatellite sequences, Mol Pathol, № 52, с. 50
    https://doi.org/10.1136/mp.52.1.50
25. Wells, Sequencing-based variant detection in the polyploid crop oilseed rape, BMC Plant Biol, № 13, с. 111
    https://doi.org/10.1186/1471-2229-13-111
26. Bowers, Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events, Nature, № 422, с. 433
    https://doi.org/10.1038/nature01521
27. Yang, Sequence-level analysis of the diploidization process in the triplicated Flowering Locus C region of Brassica rapa, Plant Cell, № 18, с. 1339
    https://doi.org/10.1105/tpc.105.040535
28. Choi, Current status of Korean ginseng (Panax ginseng) genome mapping and sequencing, с. 762

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