biologia plantarum

International journal on Plant Life established by Bohumil Němec in 1959

Biologia plantarum 52:445-452, 2008 | DOI: 10.1007/s10535-008-0089-1

Localization of BAC clones on mitotic chromosomes of Musa acuminata using fluorescence in situ hybridization

E. Hřibová1, M. Doleželová1, J. Doležel1,2,*
1 Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Olomouc, Czech Republic
2 Department of Cell Biology and Genetics, Palacký University, Olomouc, Czech Republic

A bacterial artificial chromosome (BAC) library of banana (Musa acuminata) was used to select BAC clones that carry low amounts of repetitive DNA sequences and could be suitable as probes for fluorescence in situ hybridization (FISH) on mitotic metaphase chromosomes. Out of eighty randomly selected BAC clones, only one clone gave a single-locus signal on chromosomes of M. acuminata cv. Calcutta 4. The clone localized on a chromosome pair that carries a cluster of 5S rRNA genes. The remaining BAC clones gave dispersed FISH signals throughout the genome and/or failed to produce any signal. In order to avoid the excessive hybridization of repetitive DNA sequences, we subcloned nineteen BAC clones and selected their 'low-copy' subclones. Out of them, one subclone gave specific signal in secondary constriction on one chromosome pair; three subclones were localized into centromeric and peri-centromeric regions of all chromosomes. Other subclones were either localized throughout the banana genome or their use did not result in visible FISH signals. The nucleotide sequence analysis revealed that subclones, which localized on different regions of all chromosomes, contained short fragments of various repetitive DNA sequences. The chromosome-specific BAC clone identified in this work increases the number of useful cytogenetic markers for Musa.

Keywords: cytogenetic mapping; chromosome structure; repetitive DNA; ribosomal DNA; subcloning
Subjects: banana; chlorophyll fluorescence; chromosomes; cultivar and genotype differences; cytogenic mapping; DNA markers; Musa acuminata

Received: July 8, 2007; Accepted: December 21, 2007; Published: September 1, 2008  Show citation

ACS AIP APA ASA Harvard Chicago Chicago Notes IEEE ISO690 MLA NLM Turabian Vancouver
Hřibová, E., Doleželová, M., & Doležel, J. (2008). Localization of BAC clones on mitotic chromosomes of Musa acuminata using fluorescence in situ hybridization. Biologia plantarum, 52(3), 445-452. doi: 10.1007/s10535-008-0089-1
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    References

    1. Aert, R., Sagi, L., Volckaert, G.: Gene content and density in banana (Musa acuminata) as revealed by genomic sequencing of BAC clones.-Theor. appl. Genet. 109: 129-139, 2004. Go to original source...
    2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.-Nucl. Acids Res. 25: 3389-3402, 1997. Go to original source...
    3. Appels, R., Gerlach, W.L., Dennis, E.S., Swift, H., Peacock, W.J.: Molecular and chromosomal organization of DNA sequences coding for the ribosomal RNAs in cereals.-Chromosoma 78: 293-311, 1980. Go to original source...
    4. Balint-Kurti, P.J., Clendennen, S.K., Doleželová, M., Valárik, M., Doležel, J., Beetham, P.R., May, G.D.: Identification and chromosomal localization of the monkey retrotransposon in Musa sp.-Mol. gen. Genet. 263: 908-915, 2000. Go to original source...
    5. Bartoš, J., Alkhimova, O., Doleželová, M., De Langhe, E., Doležel, J.: Nuclear genome size and genomic distribution of ribosomal DNA in Musa and Ensete (Musaceae): taxonomic implications.-Cytogenet. Genome Res. 109: 50-57, 2005. Go to original source...
    6. Doležel, J., Doleželová, M., Novák, F.J.: Flow cytometric estimation of nuclear DNA amount in diploid bananas (Musa acuminata and M. balbisiana).-Biol. Plant. 36: 351-357, 1994. Go to original source...
    7. Doleželová, M., Valárik, M., Swennen, R., Horry, J.P., Doležel, J.: Physical mapping of the 18S-25S and 5S ribosomal RNA genes in diploid bananas.-Biol. Plant. 41: 497-505, 1998. Go to original source...
    8. Ellis, T.N., Lee, D., Thomas, C.M., Simpson, P.R., Cleary, W.G., Newman, M.A., Burcham, K.W.G.: 5S rRNA genes in Pisum: Sequence, long range and chromosomal organization.-Mol. gen. Genet. 214: 333-342, 1988. Go to original source...
    9. Hanson, R.E., Zwick, M.S., Choi, S.D., Islam-Faridi, M.N., McKnight, T.D., Wing, R.A., Price, H.J., Stelly, D.M.: Fluorescent in situ hybridization of a bacterial artificial chromosome.-Genome 38: 646-651, 1995. Go to original source...
    10. Hasterok, R., Marasek, A., Donnison, I.S., Armstead, I., Thomas, A., King, I.P., Wolny, E., Idziak, D., Draper, J., Jenkins, G.: Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization.-Genetics 173: 349-362, 2006. Go to original source...
    11. Janda, J., Šafář, J., Kubaláková, M., Bartoš, J., Kovářová, P., Suchánková, P., Pateyron, S., Číhalíková, J., Sourdille, P., Šimková, H., Faivre-Rampant, P., Hřibová, E., Bernard, M., Lukaszewski, A., Doležel, J., Chalhoub, B.: Advanced resources for plant genomics: a BAC library specific for the short arm of wheat chromosome 1B.-Plant J. 47: 977-986, 2006. Go to original source...
    12. Jiang, J.M., Gill, B.S., Wang, G.L., Ronald, P.C., Ward, D.C.: Metaphase and interphase fluorescence in-situ hybridization mapping of the rice genome with bacterial artificial chromosomes.-Proc. nat. Acad. Sci. USA 92: 4487-4491, 1995. Go to original source...
    13. Kim, J.-S., Childs, K.L., Islam-Faridi, N., Menz, M.A., Klein, R.R., Klein, P.E., Price, H.J., Mullet, J.E., Stelly, D.M.: Integrated karyotyping of sorghum by in situ hybridization of landed BACs.-Genome 45: 402-412, 2002. Go to original source...
    14. Lamb, J.C., Danilova, T., Bauer, M.J., Meyer, J.M., Holland, J.J., Jensen, M.D., Birchler, J.A.: Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes.-Genetics 175: 1047-1058, 2007. Go to original source...
    15. Lapitan, N.L.V., Brown, S.E., Kennard, W., Stephens, J.L., Knudson, D.L.: FISH physical mapping with barley BAC clones.-Plant J. 11: 149-156, 1997. Go to original source...
    16. Lehfer, H., Bush, W., Martin, R., Herrman, R.G.: Localization of the B-hordein locus on barley chromosomes using fluorescence in situ hybridization.-Chromosoma 102: 428-432, 1993. Go to original source...
    17. Lengerová, M., Kejnovsky, E., Hobza, R., Macas, J., Grant, S.R., Vyskot, B.: Multicolor FISH mapping of the dioecious model plant, Silene latifolia.-Theor. appl. Genet. 108: 1193-1199, 2004. Go to original source...
    18. Long, E.O., Dawid, I.B.: Repeated genes in eukaryotes.-Annu. Rev. Biochem. 49: 727-764, 1980. Go to original source...
    19. Lysák, M.A., Fransz, P.F., Ali, H.B.M., Schubert, I.: Chromosome painting in Arabidopsis thaliana.-Plant J 28: 689-697, 2001. Go to original source...
    20. Mokroš, P., Vrbský, J., Široký, J.: Identification of chromosomal fusion sites in Arabidopsis mutants using sequential bicolour BAC-FISH.-Genome 49: 1036-1042, 2006. Go to original source...
    21. Navrátilová, A., Neumann, P., Macas, J.: Karyotype analysis of four Vicia species using in situ hybridization with repetitive sequences.-Ann. Bot. 91: 921-926, 2003. Go to original source...
    22. Ndowora, T., Dahal, G., LaFleur, D., Harper, G., Hull, R., Olszewski, N.E., Lockhart, B.: Evidence that badnavirus infection in Musa can originate from integrated pararetroviral sequences.-Virology 255: 214-220, 1999. Go to original source...
    23. Ortiz-Vazquez, E., Kaemmer, D., Zhang, H.B., Muth, J., Rodriguez-Mendiola, M., Arias-Castro, C., James, A.: Construction and characterization of a plant transformation-competent BIBAC library of the black Sigatoka-resistant banana Musa acuminata cv. Tuu Gia (AA).-Theor. appl. Genet. 110: 706-713, 2005. Go to original source...
    24. Osuji, J.O., Crouch, J., Harrison, G., Heslop-Harrison, J.S.: Molecular cytogenetics of Musa species, cultivars and hybrids: location of 18S-5.8S-25S and 5S rDNA and telomere-like sequences.-Ann. Bot. 82: 243-248, 1998. Go to original source...
    25. Pedersen, C., Rasmussen, S.K., Linde-Laursen, I.: Genome and chromosome identification in cultivated barley and related species of the Triticeae (Poaceae) by in situ hybridization with the GAA-satellite sequence.-Genome 39: 93-104, 1996. Go to original source...
    26. Šafář, J., Noa-Carrazana, J.C., Vrána, J., Bartoš, J., Alkhimova, O., Sabau, X., Šimková, H., Lheureux, F., Caruana, M.L., Doležel, J., Piffanelli, P.: Creation of a BAC resource to study the structure and evolution of the banana (Musa balbisiana) genome.-Genome 47: 1182-1191, 2004. Go to original source...
    27. Sambrook, J., Fritsch, E., Maniatis, T.: Molecular Cloning: a Laboratory Manual. 2nd Edition.-Cold Spring Harbor Press, Cold Spring Harbor 1989.
    28. Simmonds, N.W., Weatherup, S.T.C.: Numerical taxonomy of the wild bananas (Musa).-New Phytol. 115: 567-571, 1990. Go to original source...
    29. Song, J., Dong, F., Jiang, J.: Construction of a bacterial artificial chromosome (BAC) library for potato molecular cytogenetics research.-Genome 43: 199-204, 2000. Go to original source...
    30. Sonnhammer, E.L.L., Durbin, R.: A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.-Gene 167: GC1-10, 1995. Go to original source...
    31. Staden, R., Beal, K.F., Bonfield, J.K.: The Staden package, 1998.-Methods mol. Biol. 132: 115-130, 2000. Go to original source...
    32. Tsuimoto, H., Mukai, Y., Akagawa, K., Nagaki, K., Fujigaki, J., Yamamoto, M., Sasakuma, T.: Identification of individual barley chromosomes based on repetitive sequences: Conservative distribution of Afa-family repetitive sequences on the chromosomes of barley and wheat.-Gene Genet. Syst. 72: 3003-309, 1997. Go to original source...
    33. Valárik, M., Bartoš, J., Kovářová, P., Kubaláková, M., De Jong, J.H., Doležel, J.: High-resolution FISH on super-stretched flow-sorted plant chromosomes.-Plant J. 37: 940-950, 2004. Go to original source...
    34. Valárik, M., Šimková, H., Hřibová, E., Šafář, J., Doleželová, M., Doležel, J.: Isolation, characterization and chromosome localization of repetitive DNA sequences in bananas (Musa ssp.).-Chromosome Res 10: 89-100, 2002. Go to original source...
    35. Vilarinhos, A., Carrel, F., Rodier, M., Hippolyte, I., Benabdelmouna, A., Triaire, D., Bakry, F., Courtois, B., D'Hont, A.: Characterization of translocations in banana by FISH of BAC clones anchored to a genetic map.-In: Abstracts of the International Conference "Plant and Animal Genome XIV". P. 8. Sherago International, San Diego 2006.
    36. Vilarinhos, A.D., Piffanelli, P., Lagoda, P., Thibivilliers, S., Sabau, X., Carreel, F., D'Hont, A.: Construction and characterization of a bacterial artificial chromosome library of banana (Musa acuminata Colla).-Theor. appl. Genet. 106: 1102-1106, 2003. Go to original source...
    37. Yuan, Y., Sanmiguel, P.J., Bennetzen, J.L.: High-Cot sequence analysis of the maize genome.-Plant J. 34: 249-255, 2003. Go to original source...
    38. Zhang, P., Li, W.L., Fellers, J., Friebe, B., Gill, B.S.: BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements.-Chromosoma 112: 288-299, 2004. Go to original source...

    Return to the content