Advertisement

Genes & Genomics

, Volume 41, Issue 7, pp 839–847 | Cite as

Pre-labelled oligo probe-FISH karyotype analyses of four Araliaceae species using rDNA and telomeric repeat

  • Hui Chao Zhou
  • Remnyl Joyce Pellerin
  • Nomar Espinosa Waminal
  • Tae-Jin YangEmail author
  • Hyun Hee KimEmail author
Research Article
  • 115 Downloads

Abstract

Background

The family Araliaceae contains many medicinal species including ginseng of which the whole genome sequencing analyses have been going on these days.

Objective

To characterize the chromosomal distribution of 5S and 45S rDNAs and telomeric repeat in four ginseng related species of Aralia elata (Miq.) Seem., Dendropanax morbiferus H. Lév., Eleutherococcus sessiliflorus (Rupr. Et Maxim.) Seem., Kalopanax septemlobus (Thunb. ex A.Murr.) Koidz.

Method

Pre-labelled oligoprobe (PLOP)-fluorescence in situ hybridization (FISH) was carried out.

Results

The chromosome number of A. elata was 2n = 24, whereas that of the other three species of D. morbiferus, E. sessiliflorus, and K. septemlobus was 2n = 48, corresponding to diploid and tetraploid, respectively, based on the basic chromosome number x = 12 in Araliaceae. In all four species, one pair of 5S signals were detected in the proximal regions of the short arms of chromosome 3, whereas in K. septemlobus, the 5S rDNA signals localized in the subtelomeric region of short arm of chromosome 3, while all the 45S rDNA signals localized at the paracentromeric region of the short arm of chromosome 1. And the telomeric repeat signals were detected at the telomeric region of both short and long arms of most chromosomes.

Conclusion

The PLOP-FISH was very effective compared with conventional FISH method. These results provide useful comparative cytogenetic information to better understand the genome structure of each species and will be useful to trace the history of ginseng genomic constitution.

Keywords

PLOP-FISH 5S and 45S rDNA Telomeric repeat Karyotype Araliaceae 

Notes

Acknowledgements

This work was carried out with the support of the Cooperative Research Program for Agriculture Science & Technology Development (PJ01311902), Rural Development Administration, Republic of Korea.

References

  1. Adams S, Leitch I, Bennett M, Leitch A (2000) Aloe L.—a second plant family without (TTTAGGG)n telomeres. Chromosoma 109:201–205CrossRefGoogle Scholar
  2. Appels R, Honeycutt R (1986) rDNA: evolution over a billion years. DNA systematics. CRC Press, Boca Raton, pp 81–125Google Scholar
  3. Bajer A (1959) Change of length and volume of mitotic chromosomes in living cells. Hereditas 45:579–596CrossRefGoogle Scholar
  4. Belandres HR, Waminal NE, Hwang YJ, Park BS, Lee SS, Huh JH, Kim HH (2015) FISH karyotype and GISH meiotic pairing analyses of a stable intergeneric hybrid xBrassicoraphanus line BB#5. Korean J Hortic Sci Technol 33:83–92CrossRefGoogle Scholar
  5. Berjano R, Roa F, Talavera S, Guerra M (2009) Cytotaxonomy of diploid and polyploid Aristolochia (Aristolochiaceae) species based on the distribution of CMA/DAPI bands and 5S and 45S rDNA sites. Plant Syst Evol 280:219–227CrossRefGoogle Scholar
  6. Biscotti MA, Olmo E, Heslop-Harrison JP (2015) Repetitive DNA in eukaryotic genomes. Chromosome Res 23:415–420CrossRefGoogle Scholar
  7. Cai Q, Zhang D, Zl L, Wang Xr (2006) Chromosomal localization of 5S and 18S rDNA in five species of subgenus Strobus and their implications for genome evolution of Pinus. Ann Bot 97:715–722CrossRefGoogle Scholar
  8. Choi Y, Ko S, Lee K, Yoon E (2002) Production of plantlets of Eleutherococcus sessiliflorus via somatic embryogenesis and successful transfer to soil. Plant Cell Tissue Org Cult 69:201–204CrossRefGoogle Scholar
  9. Chung MC, Lee YI, Cheng YY, Chou YJ, Lu CF (2008) Chromosomal polymorphism of ribosomal genes in the genus Oryza. Theor Appl Genet 116:745–753CrossRefGoogle Scholar
  10. Da Silva CRM, Quintas CC, Vanzela ALL (2010) Distribution of 45S and 5S rDNA sites in 23 species of Eleocharis (Cyperaceae). Genetica 138:951–957CrossRefGoogle Scholar
  11. Dong F, Naess SongSJ, Helgeson K, Gebhardt JP, Jiang C J (2000) Development and applications of a set of chromosome-specific cytogenetic DNA markers in potato. Theor Appl Genet 101:1001–1007CrossRefGoogle Scholar
  12. Fajkus P, Peska V, Sitova Z, Fulneckova J, Dvorackova M, Gogela R, Sykorova E, Hapala J, Fajkus J (2016) Allium telomeres unmasked: the unusual telomeric sequence (CTCGGTTATGGG)n is synthesized by telomerase. Plant J 85:337–347CrossRefGoogle Scholar
  13. Fregonezi JN, Fernandes T, Torezan JMD, Vieira AOS, Vanzela ALL (2006) Karyotype differentiation of four Cestrum species (Solanaceae) based on the physical mapping of repetitive DNA. Genet Mol Biol 29:97–104CrossRefGoogle Scholar
  14. Fuchs J, Brandes A, Schubert I (1995) Telomere sequence localization and karyotype evolution in higher plants. Plant Syst Evol 196:227–241CrossRefGoogle Scholar
  15. Galian JA, Rosato M, Rossello JA (2012) Early evolutionary colocalization of the nuclear ribosomal 5S and 45S gene families in seed plants: evidence from the living fossil gymnosperm Ginkgo biloba. Heredity 108:640–646CrossRefGoogle Scholar
  16. Garcia S, Garnatje T, Pellicer J, McArthur ED, Siljak-Yakovlev S, Valles J (2009) Ribosomal DNA, heterochromatin, and correlation with genome size in diploid and polyploid North American endemic sagebrushes (Artemisia, Asteraceae). Genome 52:1012–1024CrossRefGoogle Scholar
  17. Garcia S, Kovařík A, Leitch AR, Garnatje T (2017) Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database. Plant J 89:1020–1030CrossRefGoogle Scholar
  18. Guerra M (2012) Cytotaxonomy: the end of childhood. Plant Biosyst 146:703–710Google Scholar
  19. Guetat A, ROSATO M, Rossello JA, Boussaid M (2015) Karyotype analysis in Allium roseum L.(Alliaceae) using fluorescent in situ hybridization of rDNA sites and conventional stainings. Turk J Bot 39:796–807CrossRefGoogle Scholar
  20. Hasterok R, Jenkins G, Langdon T, Jones RN, Maluszynska J (2001) Ribosomal DNA is an effective marker of Brassica chromosomes. Theor Appl Genet 103:486–490CrossRefGoogle Scholar
  21. He Q, Cai Z, Hu T, Liu H, Bao C, Mao W, Jin W (2015) Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.). BMC Plant Biol 15:105CrossRefGoogle Scholar
  22. Heslop-Harrison J (2000) Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 12:617–635CrossRefGoogle Scholar
  23. Heywood VH (2014) The socio-economic importance of the Apiales. J Fac Pharm Istanbul 44:113–130Google Scholar
  24. Hizume M, Shibata F, Matsusaki Y, Kond T (2000) Chromosomal localization of telomere sequence repeats in five gymnosperm species. Chromosome Sci 4:39–42Google Scholar
  25. Hwang HS, Choi YE (2016) Phylogenetic analysis of 14 Korean Araliaceae species using chloroplast DNA barcode analysis. J Plant Biotechnol 43:82–90CrossRefGoogle Scholar
  26. Hwang Y, Kim H, Kwon S, Yang T, Ko H, Park B, Chung J, Lim K (2009) Karyotype analysis of three Brassica species using five different repetitive DNA markers by fluorescence in situ hybridization. Hortic Environ Biotechnol 27:456–463Google Scholar
  27. Hwang YJ, Lee SN, Song KA, Ryu KB, Ryu KH, Kim HH (2010) Karyotype analyses of genetically modified (GM) and Non-GM hot peppers by conventional staining and FISH method. Hortic Environ Biotechnol 51:525–530Google Scholar
  28. Hyun TK, Kim M-o, Lee H, Kim Y, Kim E, Kim J-S (2013) Evaluation of anti-oxidant and anti-cancer properties of Dendropanax morbifera Léveille. Food Chem 141:1947–1955CrossRefGoogle Scholar
  29. Ilnicki T (2014) Plant biosystematics with the help of cytology and cytogenetics. Caryologia 67:199–208CrossRefGoogle Scholar
  30. Kannan TP, Zilfalil BA (2009) Cytogenetics: past, present and future. Malays J Med Sci: MJMS 16:4Google Scholar
  31. Kato A, Vega JM, Han F, Lamb JC, Birchler JA (2005) Advances in plant chromosome identification and cytogenetic techniques. Curr Opin Plant Biol 8:148–154CrossRefGoogle Scholar
  32. Kato A, Kato A, Albert P, Vega J, Kato A, Albert P, Vega J, Birchler J (2006) Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation. Biotech Histochem 81:71–78CrossRefGoogle Scholar
  33. Kejnovsky E, Kubat Z, Macas J, Hobza R, Mracek J, Vyskot B (2006) Retand: a novel family of gypsy-like retrotransposons harboring an amplified tandem repeat. Mol Genet Genom 276:254–263CrossRefGoogle Scholar
  34. Khrolenko YA, Burundukova O (2013) Ecological features of the leaf structure and plastid apparatus of Far East Araliaceae species. Contemp Probl Ecol 6:374–380CrossRefGoogle Scholar
  35. Kiefer D, Pantuso T (2003) Panax ginseng. Am Fam Physician 68:1539–1542Google Scholar
  36. Kim JS, Shim SH, Chae S, Han SJ, Kang SS, Son KH, Chang HW, Kim HP, Bae K (2005) Saponins and other constituents from the leaves of Aralia elata. Chem Pharm Bull 53:696–700CrossRefGoogle Scholar
  37. Kim K, Nguyen VB, Dong J, Wang Y, Park JY, Lee SC, Yang TJ (2017) Evolution of the Araliaceae family inferred from complete chloroplast genomes and 45S nrDNAs of 10 Panax-related species. Sci Rep 7:4917CrossRefGoogle Scholar
  38. Kolano B, Siwinska D, McCann J, Weiss Schneeweiss H (2015) The evolution of genome size and rDNA in diploid species of Chenopodium s.l. (Amaranthaceae). Bot J Linn Soc 179:218–235CrossRefGoogle Scholar
  39. Kubis S, Schmidt T, Heslop-Harrison JS (1998) Repetitive DNA elements as a major component of plant genomes. Ann Bot 82:45–55CrossRefGoogle Scholar
  40. Kulak S, Hasterok R, Maluszynska J (2002) Karyotyping of Brassica amphidiploids using 5S and 25S rDNA as chromosome markers. Hereditas 136:144–150CrossRefGoogle Scholar
  41. Lakshmanan PS, Van Laere K, Eeckhaut T, Van Huylenbroeck J, Van Bockstaele E, Khrustaleva L (2015) Karyotype analysis and visualization of 45S rRNA genes using fluorescence in situ hybridization in aroids (Araceae). Comp Cytogenet 9:145–160CrossRefGoogle Scholar
  42. Lavania UC, Kushwaha JS, Lavania S, Basu S (2010) Chromosomal localization of rDNA and DAPI bands in solanaceous medicinal plant Hyoscyamus niger L. J Genet 89:493CrossRefGoogle Scholar
  43. Lee DK, Kang HS (2002) Distribution of Kalopanax septemlobus and its growth in Northeast Asia. Eurasian J For Res 5:85–94Google Scholar
  44. Lee YS, Park HM, Kim N-H, Waminal NE, Kim YJ, Lim K-B, Baek JH, Kim HH, Yang T-J (2015) Phylogenetic relationship of 40 species of genus Aloe L. and the origin of an allodiploid species revealed by nucleotide sequence variation in chloroplast intergenic space and cytogenetic in situ hybridization. Genet Resour Crop Evol 63:1–8Google Scholar
  45. Levan A, Fredga K, Sandberg AA (1964) Nomenclature for centromeric position on chromosomes. Hereditas 52:201–220CrossRefGoogle Scholar
  46. Lim KY, Matyášek R, Lichtenstein CP, Leitch AR (2000) Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae. Chromosoma 109:245–258CrossRefGoogle Scholar
  47. Lima-de-Faria A (1976) The chromosome field: I. Prediction of the location of ribosomal cistrons. Hereditas 83:1–22CrossRefGoogle Scholar
  48. Maluszynska J, Heslop-Harrison J (1993) Physical mapping of rDNA loci in Brassica species. Genome 36:774–781CrossRefGoogle Scholar
  49. Mizuochi H, Marasek A, Okazaki K (2007) Molecular cloning of Tulipa fosteriana rDNA and subsequent FISH analysis yields cytogenetic organization of 5S rDNA and 45S rDNA in T. gesneriana and T. fosteriana. Euphytica 155:235CrossRefGoogle Scholar
  50. Moscone EA, Loidl J, Ehrendorfer F, Hunziker AT (1995) Analysis of active nucleolus organizing regions in Capsicum (Solanaceae) by silver staining. Am J Bot 82:276–287CrossRefGoogle Scholar
  51. Nemeth AV, Dudits D, Molnar-Lang M, Linc G (2013) Molecular cytogenetic characterisation of Salix viminalis L. using repetitive DNA sequences. J Appl Genet 54:265–269CrossRefGoogle Scholar
  52. Ohnishi H, Yamamoto MT (2004) The structure of a single unit of ribosomal RNA gene (rDNA) including intergenic subrepeats in the Australian bulldog ant Myrmecia croslandi (Hymenoptera: Formicidae). Zool Sci 21:139–146CrossRefGoogle Scholar
  53. Östergren G (1944) Colchicine mitosis, chromosome contraction, narcosis and protein chain folding. Hereditas 30:429–467CrossRefGoogle Scholar
  54. Park BY, Min BS, Oh SR, Kim JH, Kim TJ, Kim DH, Bae KH, Lee HK (2004) Isolation and anticomplement activity of compounds from Dendropanax morbifera. J Ethnopharmacol 90:403–408CrossRefGoogle Scholar
  55. Park SY, Cho HM, Moon HK, Kim YW, Paek KY (2011) Genotypic variation and aging effects on the embryogenic capability of Kalopanax septemlobus. Plant Cell Tissue Organ Cult 105:265–270CrossRefGoogle Scholar
  56. Pellerin R, Waminal N, Kim H (2019) FISH mapping of rDNA and telomeric repeats in 10 Senna species. Hortic Environ Biotechnol.  https://doi.org/10.1007/s13580-018-0115-y Google Scholar
  57. Peng D, Chen W, Xie J (2008) Antihyperglycemic effects of ginseng and possible mechanisms. Drugs Future 33:507–514CrossRefGoogle Scholar
  58. Peška V, Fajkus P, Fojtová M, Dvořáčková M, Hapala J, Dvořáček V, Polanská P, Leitch AR, Sýkorová E, Fajkus J (2015) Characterisation of an unusual telomere motif (TTTTTTAGGG) n in the plant Cestrum elegans (Solanaceae), a species with a large genome. Plant J 82:644–654CrossRefGoogle Scholar
  59. Philipson WR (1979) Araliaceae—I. Flora Malesiana-1 9:1–105Google Scholar
  60. Pita M, Orellana J, Martinez-Rodriguez P, Martinez-Ramirez A, Fernandez-Calvin B, Bella JL (2014) FISH methods in cytogenetic studies. Methods Mol Biol 1094:109–135CrossRefGoogle Scholar
  61. Plohl M, Luchetti A, Mestrovic N, Mantovani B (2008) Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero) chromatin. Gene 409:72–82CrossRefGoogle Scholar
  62. Plunkett GM, Wen J, Lowry Ii PP (2004) Infrafamilial classifications and characters in Araliaceae: Insights from the phylogenetic analysis of nuclear (ITS) and plastid (trnL-trnF) sequence data. Plant Syst Evol 245:1–39CrossRefGoogle Scholar
  63. Richards EJ, Ausubel FM (1988) Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell 53:127–136CrossRefGoogle Scholar
  64. Roa F, Guerra M (2012) Distribution of 45S rDNA sites in chromosomes of plants: structural and evolutionary implications. BMC Evol Biol 12:225–237CrossRefGoogle Scholar
  65. Robledo G, Lavia G, Seijo G (2009) Species relations among wild Arachis species with the A genome as revealed by FISH mapping of rDNA loci and heterochromatin detection. Theor Appl Genet 118:1295–1307CrossRefGoogle Scholar
  66. Seijo J, Lavia G, Fernandez A, Krapovickas A, Ducasse D, Moscone E (2004) Physical mapping of the 5S and 18S-25S rRNA genes by FISH as evidence that Arachis duranensis and A. ipaensis are the wild diploid progenitors of A. hypogaea (Leguminosae). Am J Bot 91:1294–1303CrossRefGoogle Scholar
  67. Sharma S, Raina S (2005) Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes. Cytogenet Genome Res 109:15–26CrossRefGoogle Scholar
  68. Shibata F, Matsusaki Y, Hizume M (2005) AT-rich sequences containing Arabidopsis-type telomere sequence and their chromosomal distribution in Pinus densiflora. Theor Appl Genet 110:1253–1258CrossRefGoogle Scholar
  69. Shohael A, Chakrabarty D, Ali M, Yu K, Hahn E, Lee H, Paek K (2006) Enhancement of eleutherosides production in embryogenic cultures of Eleutherococcus sessiliflorus in response to sucrose-induced osmotic stress. Process Biochem 41:512–518CrossRefGoogle Scholar
  70. Silahtaroglu A, Pfundheller H, Koshkin A, Tommerup N, Kauppinen S (2004) LNA-modified oligonucleotides are highly efficient as FISH probes. Cytogenet Genome Res 107:32–37CrossRefGoogle Scholar
  71. Suh S-J, Jin U-H, Kim K-W, Son J-K, Lee SH, Son K-H, Chang HW, Lee Y-C, Kim C-H (2007) Triterpenoid saponin, oleanolic acid 3-O-β-d-glucopyranosyl (1→ 3)-α-l-rhamnopyranosyl (1→ 2)-α-l-arabinopyranoside (OA) from Aralia elata inhibits LPS-induced nitric oxide production by down-regulated NF-κB in raw 264.7 cells. Arch Biochem Biophys 467:227–233CrossRefGoogle Scholar
  72. Sun BY, Kim CH, Soh WY (1988) Chromosome numbers of Araliaceae in Korea. Korean J Plant Taxon 18:291–291CrossRefGoogle Scholar
  73. Sykorova E, Lim KY, Chase MW, Knapp S, Leitch IJ, Leitch AR, Fajkus J (2003) The absence of Arabidopsis-type telomeres in Cestrum and closely related genera Vestia and Sessea (Solanaceae): first evidence from eudicots. Plant J 34:283–291CrossRefGoogle Scholar
  74. Tran TD, Cao HX, Jovtchev G, Neumann P, Novák P, Fojtová M, Vu GTH, Macas J, Fajkus J, Schubert I et al (2015) Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea. Plant J 84:1087–1099CrossRefGoogle Scholar
  75. Vitales D, D’Ambrosio U, Gálvez F, Kovařík A, Garcia S (2017) Third release of the plant rDNA database with updated content and information on telomere composition and sequenced plant genomes. Plant Syst Evol 303:1115–1121CrossRefGoogle Scholar
  76. Waminal NE, Kim NS, Kim HH (2011) Dual-color FISH karyotype analyses using rDNAs in three Cucurbitaceae species. Genes Genom 33:521–528CrossRefGoogle Scholar
  77. Waminal NE, Kim HH (2012) Dual-color FISH karyotype and rDNA distribution analyses on four Cucurbitaceae species. Hortic Environ Biotechnol 53:49–56CrossRefGoogle Scholar
  78. Waminal NE, Kim HH (2015) FISH Karyotype analysis of four wild Cucurbitaceae species using 5S and 45S rDNA probes and the emergence of new polyploids in Trichosanthes kirilowii Maxim. Korean J Hortic Sci Technol 33:869–876CrossRefGoogle Scholar
  79. Waminal NE, Choi H-I, Kim N-H, Jang W, Lee J, Park JY, Kim HH, Yang T-J (2016) A refined Panax ginseng karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs. J Ginseng Res 41:469–476CrossRefGoogle Scholar
  80. Waminal NE, Pellerin RJ, Kim N-S, Jayakodi M, Park JY, Yang T-J, Kim HH (2018) Rapid and efficient FISH using pre-labeled oligomer probes. Sci Rep 8:8224CrossRefGoogle Scholar
  81. Wen J, Plunkett GM, Mitchell AD, Wagstaff SJ (2001) The evolution of Araliaceae: a phylogenetic analysis based on ITS sequences of nuclear ribosomal DNA. Syst Bot 26:144–167Google Scholar
  82. Yi T, Ii PPL, Plunkett GM, Wen J (2004) Chromosomal evolution in Araliaceae and close relatives. Taxon 53:987CrossRefGoogle Scholar
  83. Youn SM, Kim HH (2018) Chromosome karyotyping of Senna covesii and S. floribunda based on triple-color FISH mapping of rDNAs and telomeric repeats. Plant Breed Biotechnol 6:51–56CrossRefGoogle Scholar
  84. Zhang D, Yang Q, Ding Y, Cao X, Xue Y, Cheng Z (2008) Cytological characterization of the tandem repetitive sequences and their methylation status in the Antirrhinum majus genome. Genomics 92:107–114CrossRefGoogle Scholar
  85. Zhang ZT, Yang SQ, Li ZA, Zhang YX, Wang YZ, Cheng CY, Li J, Chen JF, Lou QF (2016) Comparative chromosomal localization of 45S and 5S rDNAs and implications for genome evolution in Cucumis. Genome 59:449–457CrossRefGoogle Scholar
  86. Zhou HC, Park EJ, Kim HH (2018) Analysis of chromosome composition of Gastrodia elata Blume by fluorescent in situ hybridization using rDNA and telomeric repeat probes. Korean J Crop Sci 26:113–118Google Scholar

Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  1. 1.Department of Life Sciences, Chromosome Research InstituteSahmyook UniversitySeoulRepublic of Korea
  2. 2.Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea

Personalised recommendations