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http://dx.doi.org/10.1016/j.jgr.2016.08.002

A refined Panax ginseng karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs  

Waminal, Nomar Espinosa (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Choi, Hong-Il (Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute)
Kim, Nam-Hoon (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of 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 of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Lee, Junki (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Park, Jee Young (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Kim, Hyun Hee (Department of Life Science, Plant Biotechnology Institute, Sahmyook University)
Yang, Tae-Jin (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Publication Information
Journal of Ginseng Research / v.41, no.4, 2017 , pp. 469-476 More about this Journal
Abstract
Background: Panax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification. Methods: Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR. Results: Recently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4',6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype. Conclusion: Identification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.
Keywords
FISH; karyotype; Panax ginseng; Pg167TR; tandem repeats;
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1 Michael TP, Jackson S. The first 50 plant genomes. Plant Genom 2013;6:1-7.
2 Macas J, Koblízkova A, Navratilova A, Neumann P. Hypervariable 3' UTR region of plant LTR-retrotransposons as a source of novel satellite repeats. Gene 2009;448:198-206.   DOI
3 Choi HI, Waminal NE, Park HM, Kim NH, Choi BS, Park M, Choi D, Lim YP, Kwon SJ, Park BS, et al. Major repeat components covering one-third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy. Plant J 2014;77:906-16.   DOI
4 Coluccia E, Pichiri G, Nieddu M, Coni P, Manconi S, Deiana AM, Salvadori S, Mezzanotte R. Identification of two new repetitive elements and chromosomal mapping of repetitive DNA sequences in the fish Gymnothorax unicolor (Anguilliformes: Muraenidae). Eur J Histochem 2011;55:e12.
5 Sharma A, Wolfgruber TK, Presting GG. Tandem repeats derived from centromeric retrotransposons. BMC Genomics 2013;14:142.   DOI
6 Mehrotra S, Goyal V. Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function. Genomics Proteomics Bioinformatics 2014;12:164-71.   DOI
7 Mondin M, Santos-Serejo JA, Bertao MR, Laborda P, Pizzaia D, Aguiar-Perecin ML. Karyotype variability in tropical maize sister inbred lines and hybrids compared with KYS standard line. Front Plant Sci 2014;5:544.
8 Palomeque T, Lorite P. Satellite DNA in insects: a review. Heredity 2008;100:564-73.   DOI
9 Plohl M, Luchetti A, Mestrovic N, Mantovani B. Satellite DNAs between self-ishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 2008;409:72-82.   DOI
10 Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, et al. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol 2013;14:R10.   DOI
11 Koo DH, Hong CP, Batley J, Chung YS, Edwards D, Bang JW, Hur Y, Lim YP. Rapid divergence of repetitive DNAs in Brassica relatives. Genomics 2011;97:173-85.   DOI
12 Ananiev EV, Phillips RL, Rines HW. Complex structure of knob DNA on maize chromosome 9: retrotransposon invasion into heterochromatin. Genetics 1998;149:2025-37.
13 Smith DR. Random primed labeling of DNA. Methods Mol Biol 1993;18:445-7.
14 Matyasek R, Gazdova B, Fajkus J, Bezdek M. NTRS, a new family of highly repetitive DNAs specific for the T1 chromosome of tobacco. Chromosoma 1997;106:369-79.   DOI
15 Mendes S, Moraes AP, Mirkov TE, Pedrosa-Harand A. Chromosome homeologies and high variation in heterochromatin distribution between Citrus L. and Poncirus Raf. as evidenced by comparative cytogenetic mapping. Chromosome Res 2011;19:521-30.   DOI
16 Xiong Z, Pires JC. Karyotype and identification of all homoeologous chromosomes of allopolyploid Brassica napus and its diploid progenitors. Genetics 2011;187:37-49.   DOI
17 Albert PS, Gao Z, Danilova TV, Birchler JA. Diversity of chromosomal karyotypes in maize and its relatives. Cytogenet Genome Res 2010;129:6-16.   DOI
18 Pita M, Orellana J, Martinez-Rodriguez P, Martinez-Ramirez A, Fernandez-Calvin B, Bella JL. FISH methods in cytogenetic studies. Methods Mol Biol 2014;1094:109-35.
19 Lion T, Haas OA. Nonradioactive labeling of probe with digoxigenin by polymerase chain reaction. Anal Biochem 1990;188:335-7.   DOI
20 Rigby PW, Dieckmann M, Rhodes C, Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol 1977;113:237-51.   DOI
21 Court WE, editor. Ginseng: The genus Panax. Amsterdam, Netherlands: Hardwood Academic Publishers; 2000.
22 Park HJ, Kim DH, Park SJ, Kim JM, Ryu JH. Ginseng in traditional herbal prescriptions. J Ginseng Res 2012;36:225-41.   DOI
23 Rozen S, Skaletsky HJ. Primer3 [Internet]. 1998. Available from: http://biotools.umassmed.edu/bioapps/primer3_www.cgi.
24 Leung KW, Wong AS. Pharmacology of ginsenosides: a literature review. Chin Med 2010;5:20.   DOI
25 Waminal N, 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 Cytogenet 2012;6:425-41.   DOI
26 Yi T, Lowry PP, Plunkett GM, Wen J. Chromosomal evolution in Araliaceae and close relatives. Taxon 2004;53:987-1005.   DOI
27 Kim NH, Lee SC, Choi HI, Kim K, Choi BS, Jang W, Lee J, Nomar Espinosa W, Lee YS, Park HS, et al., editors. Genome sequences and evolution of Panax ginseng. Evidence-based efficacy of ginseng 2014. Proceedings of the 11th International symposium on Ginseng. Seoul, Korea: The Korean Society of Ginseng; 2014.
28 Choi HI, Kim NH, Lee J, Choi B, Kim K, Park J, 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 2012:1-11.
29 Koo DH, Hur Y, Jin DC, Bang JW. Karyotype analysis of a Korean cucumber cultivar (Cucumis sativus L. cv. Winter Long) using C-banding and bicolor fluorescence in situ hybridization. Molecules Cells 2002;13:413-8.
30 Gerlach W, Bedbrook J. Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res 1979;7:1869-85.   DOI
31 Kato A, Albert PS, Vega JM, Birchler JA. Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation. Biotech Histochem 2006;81:71-8.   DOI
32 Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999;27:573-80.   DOI
33 Dias GB, Svartman M, Delprat A, Ruiz A, Kuhn GC. Tetris is a foldback transposon that provided the building blocks for an emerging satellite DNA of Drosophila virilis. Genome Biol Evol 2014;6:1302-13.   DOI
34 Ho IS, Leung FC. Isolation and characterization of repetitive DNA sequences from Panax ginseng. Mol Genet Genomics 2002;266:951-61.   DOI
35 Williams SM, Strobeck C. Sister chromatid exchange and the evolution of rDNA spacer length. J Theor Biol 1985;116:625-36.   DOI
36 Kato A, Lamb JC, Birchler JA. Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci 2004;101:13554-9.   DOI
37 Hwang Y, Kim H, Kwon S, Yang T, Ko H, Park B, Chung J, Lim K. Karyotype analysis of three Brassica species using five different repetitive DNA markers by fluorescence in situ hybridization. Hortic Environ Biotechnol 2009;27:456-63.
38 Santos LVDR, Foresti F, Wasko AP, Oliveira C, Martins C. Nucleotide sequence, genomic organization and chromosome localization of 5S rDNA in two species of Curimatidae (Teleostei, Characiformes). Genet Mol Biol 2006;29:251-6.   DOI