The Nucleus

, Volume 58, Issue 3, pp 173–184 | Cite as

Chromosome research in orchids: current status and future prospects with special emphasis from molecular and epigenetic perspective

  • Santosh Kumar Sharma
  • Yasuhiko Mukai


Having more than 25,000 species belonging to >800 genera, orchids are renowned for the abundance of morphotypes, with apparently everlasting compilation of extraordinary and fantastic adaptations, and represent a highly advanced terminal line of floral evolution in the angiosperms. The pattern of speciation and evolution in the family Orchidaceae is still elusive due to lack of information on valuable chromosome landmarks including centromeres, telomeres, nucleolar organizing regions (NORs), accessory chromosomes, structural rearrangements, eu/hetero-chromatin structure that ultimately resulted in complex genome organization. Therefore, an attempt has been made to catalog the available information on chromosome research in orchids encompassing the wide spectrum of conventional/molecular cytogenetics. Further, the recent developments in the broad scope of epi-cytogenetics involving nuclear architecture, spatial-temporal chromosomal distribution of DNA/histone modification marks, and their interplay in the formation of chromatin environment during cell division have been discussed. The application of flow-cytogenetics in unrevealing the complex genome architecture and ploidy of orchids has also been considered significantly. Further, in view of recent availability of the transcriptome and genome sequences of orchids, the potential of next-generation cytogenetics in discovery of myriad cytogenetic milestones for uncovering the mysteries of orchid’s genome and concurrent evolution has also been addressed. In particular, this review ultimately provides a broad scope and perspectives in different aspects of chromosome research on the highly evolved yet complex orchid family.


Orchid Chromosome Cytogenetics FISH Genome 



We thank Japan Society for the Promotion of Science (JSPS), Japan for providing post-doctoral fellowship (SKS, no. P13399) and Grants-in-Aid for Scientific Research (C) (YM, no. 25450006) in the field of orchid cytogenetics. Sincere thanks are also due to Prof. Maki Yamamoto, Kansai University of Welfare Sciences, Osaka, and Prof. Go Suzuki and all members of Plant Molecular Genetics Laboratory, Osaka Kyoiku University, Osaka, Japan for their constant encouragement and help. We also thank Osaka Kyoiku University, Osaka, Japan for providing the facilities. Sincere apologies to those authors whose work(s) we could not cite due to space limitations.

Compliance with ethical standards

Conflict of interest

Authors declare no conflict of interest. SKS and YM designed the theme of the study. SKS did the experiments and wrote the manuscript. YM provided valuable inputs for significant improvement of the quality of the manuscript.


  1. 1.
    Aoyama M. Karyomorphological studies in Cymbidium and its allied genera, Orchidaceae. Bull Hiroshima Bot Gard. 1989;11:1–121.Google Scholar
  2. 2.
    Arditti J. Fundamentals of orchid biology. New York: Wiley; 1992.Google Scholar
  3. 3.
    Begum R, Alam SS, Menzel G, Schmid T. Comparative molecular cytogenetics of major repetitive sequence families of three Dendrobium species (Orchidaceae) from Bangladesh. Ann Bot. 2009;104:863–72.PubMedCentralCrossRefPubMedGoogle Scholar
  4. 4.
    Bolaños-Villegas P, Chin SW, Chen FC. Meiotic chromosome behavior and capsule setting in Doritaenopsis hybrids. J Am Soc Hort Sci. 2008;133:107–16.Google Scholar
  5. 5.
    Brown RC. Lemmon BE Pollen development in orchids.3. A novel generative pole microtubule system predicts unequal pollen mitosis. J Cell Sci. 1991;99:273–81.Google Scholar
  6. 6.
    Brown RC. Lemmon BE Pollen development in orchids.4. Cytoskeleton and ultrastructure of the unequal pollen mitosis in Phalaenopsis. Protoplasma. 1992;167:183–92.CrossRefGoogle Scholar
  7. 7.
    Brown RC, Lemmon BE. Pollen mitosis in the slipper orchid Cypripedium fasciculatum. Sex Plant Reprod. 1994;7:87–94.CrossRefGoogle Scholar
  8. 8.
    Cabral JS, Felix LP, Guerra M. Heterochromatin diversity and its co-localization with 5S and 45S rDNA sites in chromosomes of four Maxillaria species (Orchidaceae). Genet Mol Biol. 2006;29:659–64.CrossRefGoogle Scholar
  9. 9.
    Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, et al. The genome sequence of the orchid Phalaenopsis equestris. Nat Genet. 2015;47:65–72.CrossRefPubMedGoogle Scholar
  10. 10.
    Cox AV, Abdelnour DG, Bennett MD, Leitch IJ. Genome size and karyotype evolution in the slipper orchids (Cypripedioideae: Orchidaceae). Am J Bot. 1998;85:681–87.CrossRefPubMedGoogle Scholar
  11. 11.
    D’emerico S, Galasso I, Pignone D, Scrugli A. Localization of rDNA loci by fluorescent in situ hybridization in some wild orchids from Italy (Orchidaceae). Caryologia. 2001;54:31–6.CrossRefGoogle Scholar
  12. 12.
    Daviña JR, Grabiele M, Cerutti JC, Hojsgaard DH, Almada RD, Insaurralde IS, et al. Chromosome studies in Orchidaceae from Argentina. Genet Mol Biol. 2009;32:811–21.PubMedCentralCrossRefPubMedGoogle Scholar
  13. 13.
    Dressler RL. Phylogeny and classification of the orchid family. Portland: Dioscorides; 1993.Google Scholar
  14. 14.
    Ehrendorfer F. Polyploidy and distribution. In: Lewis WH, editor. Polyploidy: Biological relevance. New York: Plenum Press; 1980. p. 45–60.CrossRefGoogle Scholar
  15. 15.
    Felix LP, Guerra M. Basic chromosome numbers of terrestrial orchids. Plant Syst Evol. 2005;254:131–48.CrossRefGoogle Scholar
  16. 16.
    Felix LP. GuerraM. Cytogenetics and cytotaxonomy of some Brazilian species of Cymbidioid orchids. Genet Mol Biol. 2000;23:957–78.CrossRefGoogle Scholar
  17. 17.
    Fu CH, Chen YW, Hsiao YY, Pan ZJ, Liu ZJ, Huang YM, et al. OrchidBase: a collection of sequences of the transcriptome derived from orchids. Plant Cell Physiol. 2011;52:238–43.CrossRefPubMedGoogle Scholar
  18. 18.
    Goldblatt P. Polyploidy in angiosperms: monocotyledons. In: Lewis WH, editor. Polyploidy: biological relevance. New York: Plenum Press; 1980. p. 219–32.CrossRefGoogle Scholar
  19. 19.
    Griesbach RJ. Polyploidy in Phalaenopsis orchid improvement. J Hered. 1985;76:74–5.Google Scholar
  20. 20.
    Heslop-Harrison JS. Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell. 2000;12:617–36.PubMedCentralCrossRefPubMedGoogle Scholar
  21. 21.
    Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, et al. Research on orchid biology and biotechnology. Plant Cell Physiol. 2011;52:1467–86.CrossRefPubMedGoogle Scholar
  22. 22.
    Hsu SC, Cheng TC, Bolaños-Villegas P, Chin SW, Chen FC. Pollen Meiotic Behavior in Relation to Phalaenopsis Breeding. In: Blanchard MG. editor. Proc Ist Intl Orchid Symposium Acta Hort. 2010. p. 878.Google Scholar
  23. 23.
    Hsu CC, Chung YC, Chen TC, Lee YL, Kuo YT, Tsai WC, et al. An overview of the Phalaenopsis orchid genome through BAC end sequence analysis. BMC Plant Biol. 2011;11:3.PubMedCentralCrossRefPubMedGoogle Scholar
  24. 24.
    Jones K. Cytology and the study of orchids. In: Withner CL, editor. The orchids: scientific studies. New York: Wiley; 1974. p. 383–89.Google Scholar
  25. 25.
    Jones RN, Vij SP. B chromosomes in orchids. J Orchid Soc India. 1988;2:77–85.Google Scholar
  26. 26.
    Jones WE, Kuehnle AR. Ploidy identification using flow cytometry in tissues of Dendrobium species and cultivars. Lindleyana. 1998;13:11–8.Google Scholar
  27. 27.
    Kao YY, Chang SB, Lin TY, Hsiehs CH, Chen YH, ChenWHand Chen CC. Differential accumulation of heterochromatin as a cause for karyotype variation in Phalaenopsis orchids. Ann Bot. 2001;87:387–95.CrossRefGoogle Scholar
  28. 28.
    Lan T, Albert VA. Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady’s slipper orchid. BMC Plant Biol. 2011;11:126.PubMedCentralCrossRefPubMedGoogle Scholar
  29. 29.
    Lee HC, Chiou DW, Chen WH. Dynamics of cell growth and endoreduplication during orchid flower development. Plant Sci. 2004;166:659–67.CrossRefGoogle Scholar
  30. 30.
    Lee YH. Cytology and fertility of an intergeneric orchid hybrid. J Hered. 1987;78:319–22.Google Scholar
  31. 31.
    Lee YI, Chung MC. Identification of genome relationships among Paphiopedilum species by genomic and fluorescent in situ hybridization. Acta Hortic. 2008;766:331–34.CrossRefGoogle Scholar
  32. 32.
    Leitch IJ, Kahandawala I, Suda J, Hanson L, Ingrouille MJ, Chase MW, et al. Genome size diversity in orchids: consequences and evolution. Ann Bot. 2009;104:469–81.PubMedCentralCrossRefPubMedGoogle Scholar
  33. 33.
    Lim WL, Loh CS. Endopolyploidy in Vanda Miss Joaquim (Orchidaceae). New Phytol. 2003;159:279–87.CrossRefGoogle Scholar
  34. 34.
    Lin CC, Chen YH, Chen WH, Chen CC, Kao YY. Genome organization and relationships of Phalaenopsis orchids inferred from genomic in situ hybridization. Bot Bull Acad Sin. 2005;46:339–45.Google Scholar
  35. 35.
    Lin S, Lee HC, Chen WH, Chen CC, Kao YY, Fu YM, et al. Nuclear DNA contents of Phalaenopsis sp. and Doritis pulcherrima. J Am Soc Hortic Sci. 2001;126:195–99.Google Scholar
  36. 36.
    Matsuba A, Fujii M, Lee SS, Suzuki G, Yamamoto M, Mukai Y. Molecular cytogenetic use of BAC clones of Neofinetia falcate and Rhynchostylis coelestis Nucleus. doi: 10.1007/s13237-015-0147-y.
  37. 37.
    Moscone EA, Samuel R, Schwarzacher T, Schweizer D, Pedrosa-Harand A. Complex rearrangements are involved in Cephalanthera (Orchidaceae) chromosome evolution. Chromosome Res. 2007;15:931–43.CrossRefPubMedGoogle Scholar
  38. 38.
    Nagl W. Heterochromatin elimination in the orchid Dendrobium. Protoplasma. 1983;118:234–37.CrossRefGoogle Scholar
  39. 39.
    Nagl W. Localization of amplified DNA in nuclei of the orchid Cymbidium by in situ hybridization. Experientia. 1977;33:1040–41.CrossRefGoogle Scholar
  40. 40.
    Okada H. Karyomorphological observations of Apostasia nuda and Neuwiedia veratrifolia (Apostasiaceae, Orchidaceae). J Jpn Bot. 1988;63:344–50.Google Scholar
  41. 41.
    Pan ZJ, Cheng CC, Tsai WC, Chung MC, Chen WH, Hu JM, et al. The duplicated B-class MADS-Box genes display dualistic characters in orchid floral organ identity and growth. Plant Cell Physiol. 2011;52:1515–31.CrossRefPubMedGoogle Scholar
  42. 42.
    Raven PH. The bases of angiosperm phylogeny: cytology. Ann Mo Bot Gard. 1975;62:724–64.CrossRefGoogle Scholar
  43. 43.
    Roy SC, Sharma AK. Cytological studies of Indian orchids. Proc Ind Natl Sci Acad. 1972;38:72–86.Google Scholar
  44. 44.
    Sharma AK, Chetterji AK. The chromosome numbers of few more orchid genera. Curr Sci. 1966;30:75.Google Scholar
  45. 45.
    Sharma SK, Rajkumari K, Kumaria S, Tandon P, Rao SR. Karyo-morphological characterization of natural genetic variation in some threatened Cymbidium species of Northeast India. Caryologia. 2010;63:99–105.CrossRefGoogle Scholar
  46. 46.
    Sharma SK, Kumaria S, Tandon P, Rao SR. Comparative karyomorphological study of some Indian Cymbidium Swartz, 1799 (Cymbidieae, Orchidaceae). Comp Cytogenet. 2012;6:453–65.PubMedCentralCrossRefPubMedGoogle Scholar
  47. 47.
    Sharma SK, Kumaria S, Tandon P, Rao SR. Endomitosis in tapetal cells of some cymbidiums (Orchidaceae). Nucleus. 2012;55:21–5.CrossRefGoogle Scholar
  48. 48.
    Sharma SK, Mehra P, Kumari J, Kumar S, Kumaria S, Tandon P, et al. Physical localization and probable transcriptional activity of 18S-5.8S-26S rRNA gene loci in some Asiatic cymbidiums (Orchidaceae) from north-east India. Gene. 2012;499:362–66.CrossRefPubMedGoogle Scholar
  49. 49.
    Sharma SK, Dhar J, Kumaria S, Tandon P, Rao SR. Assessment of phylogenetic inter-relationships in the genus Cymbidium (Orchidaceae) based on internal transcribed spacer region of rDNA. Gene. 2012;495:10–5.CrossRefPubMedGoogle Scholar
  50. 50.
    Sharma SK, Kumaria S, Tandon P, Rao SR. Single Primer Amplification Reaction (SPAR) methods reveal the intra-specific natural genetic variation in five species of Cymbidium (Orchidaceae). Gene. 2011;483:54–62.CrossRefPubMedGoogle Scholar
  51. 51.
    Sharma SK, Kumaria S, Tandon P, Rao SR. Assessment of genetic variation and identification of species-specific ISSR markers in five species of Cymbidium (Orchidaceae). J Plant Biochem Biotechnol. 2013;22:250–55.CrossRefGoogle Scholar
  52. 52.
    Sharma SK, Yamamoto M, Mukai Y. Immuno-cytogenetic manifestation of epigenetic chromatin modification marks in plants. Planta. 2015;241:291–301.CrossRefPubMedGoogle Scholar
  53. 53.
    Shekhar N. Cytotaxonomic studies in some Indian Orchids (Ph.D thesis). Chandigarh: Punjab University; 1984.Google Scholar
  54. 54.
    Stace CA. Cytology and cytogenetics as a fundamental taxonomic resource for the twenty and twenty first centuries. Taxon. 2000;49:451–77.CrossRefGoogle Scholar
  55. 55.
    Stebbins GL. Chromosomal evolution in higher plants. London: Edward Arnold; 1971.Google Scholar
  56. 56.
    Szlachetko D. Sistema orchidalium. Frag Flor Geob. 1995;3(Suppl):1–152.Google Scholar
  57. 57.
    Teoh SB, Ong EC. Differential meiotic behaviour in hybrid clones of Aranda. Euphytica. 1983;32:799–806.CrossRefGoogle Scholar
  58. 58.
    Teoh SB. Polyploid spore formation in diploid orchid species. Genetica. 1984;63:53–9.CrossRefGoogle Scholar
  59. 59.
    Than MMM, Pal A, Jha S. Chromosome number and modal karyotype in a polysomatic endangered orchid, Bulbophyllum auricomum Lindl., the Royal Flower of Myanmar. Plant Syst Evol. 2011;294:167–75.CrossRefGoogle Scholar
  60. 60.
    Tsai WC, Fu CH, Hsiao YY, Huang YM, Chen LJ, Wang M, et al. OrchidBase 2.0: comprehensive collection of orchidaceae floral transcriptomes. Plant Cell Physiol. 2013;54:e7.CrossRefPubMedGoogle Scholar
  61. 61.
    Vij SP, Mehra PN. Cytological studies in East Himalayan Orchidaceae III: Cypripedieae. Caryologia. 1974;27:293–300.CrossRefGoogle Scholar
  62. 62.
    Vij SP, Mehra PN. Cytological studies in the East Himalayan Orchidaceae 4: Epidendreae. Res Bull (Sci) Panjab Univ. 1976;27:51–98.Google Scholar
  63. 63.
    Vij SP, Shekhar N. Cytogenetical aspects of Indian orchids. In: Vij SP, editor. Biology, conservation, and culture of orchids. New Delhi: Affiliated East-West Press Pvt. Ltd.; 1986. p. 189–220.Google Scholar
  64. 64.
    Yang M, Loh CS. Systematic endopolyploidy in Spathoglottis plicata (Orchidaceae) development. BMC Cell Biol. 2004;5:33–9.PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Archana Sharma Foundation of Calcutta 2016

Authors and Affiliations

  1. 1.Laboratory of Plant Molecular Genetics, Division of Natural SciencesOsaka Kyoiku UniversityKashiwaraJapan

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