FISH as a chromosome identification strategy to delineate karyotypic evolution in vertebrates
DOI:
https://doi.org/10.14456/tjg.2010.7Keywords:
chromosome, FISH, vertebrate, karyotypic evolutionAbstract
Fluorescence in situ hybridization (FISH) is a powerful technique to directly localize cloned DNA probes onto chromosomes. This approach is essential to delimit cytogenetic analysis, especially in karyotypic evolution study. In this review, the various applications of this method were summarized: chromosomal localization of repetitive DNA sequence, construction of chromosome mapping with single copy DNA sequences, cross-species chromosome painting, comparative genomic hybridization and genomic in situ hybridization, allowing a rapid and comprehensive analysis of the process of chromosomal rearrangement in vertebrates. The compartmental data putting together from several applications of FISH strategies provide insight into the likely constitution of a vertebrate ancestral karyotype and lead us to understand some of the intricacies of karyotypic evolution.References
Arakawa, Y., Nishida-Umehara, C., Matsuda, Y., Sutou, S. and Suzuki, H. 2002. X-chromosomal localization of mammalian Y-linked genes in two X0 species of the Ryukyu spiny rat. Cytogenet Genome Res 99: 303–309.
Beatty, B., Mai, S. and Squire, J. 2002. FISH A Practical Approach. Oxford University Press. New York.
Bi, K. Bogart, J.P. and Fu, J. 2008. Genealogical relationships of southern Ontario polyploidy unisexual salamanders (genus Ambystoma) inferred from intergenomic exchanges and major rDNA cytotypes. Chromosome Res 16: 275–289.
Brenner, S., Elgar, G., Sandford, R., Macrae, A., Venkatesh, B. and Aparício, S. 1993. Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 366: 265–268.
Burt, D.W., Bruley, C., Dunn, I.C., Jones, C.T., Ramage, A., Law, A.S., Morrice, D.R., Paton, I.R., Smith, J., Windsor, D., Sazanov, A., Fries, R. and Waddington, D. 1999. The dynamics of chromosome evolution in birds and mammals. Nature 402: 411–413.
Burt, D.W. 2002. Origin and evolution of avian microchromosomes. Cytogenet Genome Res 96: 97–112.
Chowdhary, B.P. and Raudsepp, T. 2001. Chromosome painting in farm, pet and wild animal species. Methods Cell Sci 23: 37–55.
Crooijmans, R.P., Vrebalov, J., Dijkhof, R.J., Poel, J.J. van der and Groenen, M.A. 2000. Two dimensional screening of the Wageningen chicken BAC library. Mamm Genome 11: 360–363.
Di Meo, G.P., Perucatti, A., Floriot, S., Hayes, H., Schibler, L., Incarnato, D., Di Berardino, D., Williams, J., Cribiu, E., Eggen, A. and Iannuzzi, L. 2008. An extended river buffalo (Bubalus bubalis, 2n = 50) cytogenetic map: assignment of 68 autosomal loci by FISH-mapping and R-banding and comparison with human chromosomes. Chromosome Res 16: 827–837.
Ezaz, T., Quinn, A.E., Miura, I., Sarre, S.D., Georges, A. and Graves, J.A.M. 2005. The dragon lizard Pogona vitticeps has ZZ/ZW micro-sex chromosomes. Chromosome Res 13: 763–776.
Ezaz, T., Valenzuela, N., Grützner, F., Miura, I., Georges, A., Burke, R.L. and Graves, J.A.M. 2006. An XX/XY sex microchromosome system in a freshwater turtle, Chelodina longicollis (Testudines: Chelidae) with genetic sex determination. Chromosome Res 14: 139–150.
Ezaz, T., Moritz, B., Waters, P., Graves, J.A.M., Georges, A. and Sarre, S.D. 2009. The ZW sex microchromosomes of an Australian dragon lizard share no homology with those of other reptiles or birds. Chromosome Res 17: 965–973.
Ferguson-Smith, M.A., Yang, F., Rens, W. and O’Brien, P.C.M. 2005. The impact of chromosome sorting and painting on the comparative analysis of primate genomes. Cytogenet Genome Res 108: 112–121.
Gall, J.G. and Pardue, M.L. 1969. Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci USA 63: 378–383.
Griffin, D.K., Haberman, F., Masabanda, J.S., O'Brien, P., Bagga, M., Sazanov, A., Smith, J., Burt, D.W., Ferguson-Smith, M.A. and Wienberg, J. 1999. Micro- and macrochromosome paints generated by flow cytometry and microdissection: tools for mapping the chicken genome. Cytogenet Cell Genet 87: 278–281.
Griffin, D.K., Robertson, L.B., Tempest, H.G., Vignal, A., Fillon, V., Crooijmans, R.P., Groenen, M.A., Deryusheva, S., Gaginskaya, E., Carré, W., Waddington, D., Talbot, R., Völker, M., Masabanda, J.S. and Burt, D.W. 2008. Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution. BMC Genomics 9: 168.
Groenen, M.A., Cheng, H.H., Bumstead, N., Benkel, B.F., Briles, W.E., Burke, T., Burt, D.W., Crittenden, L.B., Dodgson, J., Hillel, J., Lamont, S., de Leon, A.P., Soller, M., Takahashi, H. and Vignal, A. 2000. A consensus linkage map of the chicken genome. Genome Res 10: 137–147.
Iannuzzi, L., Gustavsson, I., Di Meo, G.P. and Ferrera, L. 1989. High-resolution studies on late-replicating segments (G+C bands) in mammalian chromosomes. Hereditas 110: 43–50.
International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695–716.
Itoh, Y. and Mizuno, S. 2002. Molecular and cytological characterization of SspI-family repetitive sequence on the chicken W chromosome. Chromosome Res 10: 499–511.
Kallioniemi, A., Kallioniemi, O.P., Sudar, D., Rutovitz, D., Gray, J.W., Waldman, F. and Pinkel, D. 1992. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818–821.
Kawagoshi, T., Nishida, C., Ota, H., Kumazawa, Y., Endo, H. and Matsuda, Y. 2008. Molecular structures of centromeric heterochromatin and karyotypic evolution in the Siamese crocodile (Crocodylus siamensis) (Crocodylidae, Crocodylia). Chromosome Res 16: 1119–1132.
Kawai, A., Nishida-Umehara, C., Ishijima, J., Tsuda, Y., Ota, H. and Matsuda, Y. 2007. Different origins of bird and reptile sex chromosomes inferred from comparative mapping of chicken Z-linked genes. Cytogenet Genome Res 117: 92–102.
Kawai, A., Ishijima, J., Nishida-Umehara, C., Kosaka, A., Ota, H., Kohno, S.-I. and Matsuda, Y. 2009. The ZW sex chromosomes of Gekko hokouensis (Gekkonidae, Squamata) represent highly conserved homology with those of avian species. Chromosoma 118: 43–51.
Kobayashi, T., Yamada, F., Hashimoto, T., Abe, S., Matsuda, Y. and Kuroiwa, A. 2007. Exceptional minute sex-specific region in the X0 mammal, Ryukyu spiny rat. Chromosome Res 15: 175–187.
Kobayashi, T., Yamada, F., Hashimoto, T., Abe, S., Matsuda, Y. and Kuroiwa, A. 2008. Centromere repositioning in the X chromosome of X0/X0 mammals, Ryukyu spiny rat. Chromosome Res 16: 587–593.
Kumar, S. and Hedges, S.B. 1998. A molecular timescale for vertebrate evolution. Nature 392: 917–920.
Liao, D. 1999. Concerted evolution: molecular mechanism and biological implications. Am J Hum Genet 64: 24–30.
Lichter, P., Tang, C.C., Call, K., Hermanson, G., Evans, G.A., Housman, D. and Ward, D.C. 1990. High-resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 247: 64–69.
Matsubara, K., Nishida-Umehara, C., Kuroiwa, A., Tsuchiya, K. and Matsuda, Y. 2003. Identification of chromosome rearrangements between the laboratory mouse (Mus musculus) and the Indian spiny mouse (Mus platythrix) by comparative FISH analysis. Chromosome Res 11: 57–64.
Matsubara, K., Nishida-Umehara, C., Tsuchiya, K., Nukaya, D. and Matsuda, Y. 2004. Karyotypic evolution of Apodemus (Muridae, Rodentia) inferred from comparative FISH analyses. Chromosome Res 12: 383–395.
Matsubara, K., Tarui, H., Toriba, M., Yamada, K., Nishida-Umehara, C., Agata, K. and Matsuda, Y. 2006. Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes. Proc Natl Acad Sci USA 103: 18190–18195.
Matsubara, K., Yamada, K., Umemoto, S., Tsuchiya, K., Ikeda, N., Nishida, C., Chijiwa, T., Moriwaki, K. and Matsuda, Y. 2008. Molecular cloning and characterization of the repetitive DNA sequences that comprise the constitutive heterochromatin of the A and B chromosomes of the Korean field mouse (Apodemus peninsulae, Muridae, Rodentia). Chromosome Res 16: 1013–1026.
Matsuda, Y. and Chapman, V.M. 1995. Application of fluorescence in situ hybridization in genome analysis of the mouse. Electrophoresis 16: 261–272.
Matsuda, Y., Nishida-Umehara, C., Tarui, H., Kuroiwa, A., Yamada, K., Isobe, T., Ando, J., Fujiwara, A., Hirao, Y., Nishimura, O., Ishijima, J., Hayashi, A., Saito, T., Murakami, T., Murakami, Y., Kuratani, S. and Agata, K. 2005. Highly conserved linkage homology between birds and turtles: Bird and turtle chromosomes are precise counterparts of each other. Chromosome Res 13: 601–615.
Meyne, J., Baker, R.J., Hobart, H.H., Hsu, T.C., Ryder, O.A., Ward, O.G., Wiley, J.E., Wurster-Hill, D.H., Yates, T.L. and Moyzis, R.K. 1990. Distribution of non-telomeric sites of the (TTAGGG)n telomeric sequences in vertebrate chromosomes. Chromosoma 99: 3–10.
Nakamura, T., Kuroiwa, A., Nishida-Umehara, C., Matsubara, K., Yamada, F. and Matsuda, Y. 2007. Comparative chromosome painting map between two Ryukyu spiny rat species, Tokudaia osimensis and Tokudaia tokunoshimensis (Muridae, Rodentia). Chromosome Res 15: 799–806.
Nanda, I. and Schmid, M. 1994. Localization of the telomeric (TTAGGG)n sequence in chicken (Gallus domesticus) chromosomes. Cytogenet Cell Genet 65: 190–193.
Nanda, I., Shan, Z., Schartl, M., Burt, D.W., Koehler, M., Nothwang, H., Grützner, F., Paton, I.R., Windsor, D., Dunn, I., Engel, W., Staeheli, P., Mizuno, S., Haaf, T. and Schmid, M. 1999. 300 million years of conserved synteny between chicken Z and human chromosome 9. Nature Genet 21: 258–259.
Nanda, I., Volff, J.-N., Weis, S., Körting, C., Froschauer, A., Schmid, M. and Schartl, M. 2000. Amplification of a long terminal repeat-like element on the Y chromosome of the platyfish, Xiphophorus maculatus. Chromosoma 109: 173–180.
Nishida-Umehara, C., Tsuda, Y., Ishijima, J., Ando, J., Fujiwara, A., Matsuda, Y. and Griffin, D.K. 2007. The molecular basis of chromosome orthologies and sex chromosomal differentiation in palaeognathous birds. Chromosome Res 15: 721–734.
O’Meally, D., Miller, H., Patel, H.R., Graves, J.A.M. and Ezaz, T. 2010. The first cytogenetic map of the tuatara, Sphenodon punctatus. Cytogenet Genome Res 127: 213–223.
Piper, J., Rutovitz, D., Sudar, D., Kallioniemi, A., Kallioniemi, O.P., Waldman, F.M., Gray, J.W. and Pinkel, D. 1995. Computer image analysis of comparative genomic hybridization. Cytometry 19: 10–26.
Porter, C., Hamilton, M.J., Sites, JR J.W. and Baker, R.J. 1991. Location of ribosomal DNA in chromosomes of squamate reptiles: systematic and evolutionary implications. Herpetologica 47: 271–280.
Rabbitts, P., Impey, H., Heppell-Parton, A., Langford, C., Tease, C., Lowe, N., Bailey, D., Ferguson-Smith, M.A. and Carter, N. 1995. Chromosome specific paints from a high resolution flow karyotype of the mouse. Nature Genet 9: 369–375.
Schmid, M., Nanda, I., Hoehn, H., Schartl, M., Haaf, T., Buerstedde, J.M., Arakawa, H., Caldwell, R.B., Weigend, S., Burt, D.W., Smith, J., Griffin, D.K., Masabanda, J.S., Groenen, M.A., Crooijmans, R.P., Vignal, A., Fillon, V., Morisson, M., Pitel, F., Vignoles, M., Garrigues, A., Gellin, J., Rodionov, A.V., Galkina, S.A., Lukina, N.A., Ben-Ari, G., Blum, S., Hillel, J., Twito, T., Lavi, U., David, L., Feldman, M.W., Delany, M.E., Conley, C.A., Fowler, V.M., Hedges, S.B., Godbout, R., Katyal, S., Smith, C., Hudson, Q., Sinclair, A. and Mizuno, S. 2005. Second report on chicken genes and chromosomes 2005. Cytogenet Genome Res 109: 415–479.
Schueler, M.G., Higgins, A.W., Rudd, M.K., Gustashaw, K. and Willard, H. 2001. Genomic and genetic definition of a functional human centromere. Science 294: 109–115.
Schwarzacher, T., Leitch, A.R., Bennett, M.D. and Heslop-Harrison, J.S. 1989. In situ localization of parental genomes in a wide hybrid. Ann Bot 64: 315–324.
Shibusawa, M., Nishibori, M., Nishida-Umehara, C., Tsudzuki, M., Masabanda, J.S., Griffin, D.K. and Matsuda, Y. 2004. Karyotypic evolution in the Galliformes: An examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny. Cytogenet Genome Res 106: 111–119.
Silva, M., Pereira, H.S., Bento, M., Santos, A.P., Shaw, P., Delgado, M., Neves, N. and Viegas, W. 2008. Interplay of ribosomal DNA loci in nucleolar dominance: dominant NORs are up-regulated by chromatin dynamics in the wheat-rye system. PLoS ONE 3: e3824.
Singer, M.F. 1982. Highly repeated sequences in mammalian genomes. Int Rev Cytol 76: 67–112.
Skinner, B.M., Robertson, L.B.W., Temspest, H.G., Langley, E.J., Ioannou, D., Fowler, K.E., Crooijmans, R.P., Hall, A.D., Griffin, D.K. and Völker, M. 2009. Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis. BMC Genomics 10: 357.
Srikulnath, K., Nishida, C. Matsubara, K., Uno, Y., Thongpan, A. Suputtitada, S., Apisitwanich, S. and Matsuda, Y. 2009a. Karyotypic evolution in squamate reptiles: comparative gene mapping revealed highly conserved linkage homology between the butterfly lizard (Leiolepis reevesii rubritaeniata, Agamidae, Lacertilia) and the Japanese four-striped rat snake (Elaphe quadrivirgata, Colubridae, Serpentes). Chromosome Res 17: 975–986.
Srikulnath, K., Matsubara, K., Uno, Y., Thongpan, A. Suputtitada, S., Apisitwanich, S. Matsuda, Y. and Nishida, C. 2009b. Karyological characterization of the butterfly lizard (Leiolepis reevesii rubritaeniata, Agamidae, Squamata) by molecular cytogenetic approach. Cytogenet Genome Res 125: 213–223.
Sutou, S., Mitsui, Y. and Tsuchiya, K. 2001. Sex determination without the Y chromosome in two Japanese rodents Tokudaia osimensis osimensis and Tokudaia osimensis spp. Mamm Genome 12: 17–21.
Suzuki, H., Iwasa, M.A., Ishii, N., Nagaoka, H. and Tsuchiya, K. 1999. The genetic status of the insular populations of the endemic spiny rat Tokudaia osimensis (Rodentia, Muridae) of the Ryukyu Islands, Japan. Mamm Study 24: 43–50.
Takahashi, E., Hori, T., O’Connell, P., Leppert, M. and White, R. 1990. R-banding and non-isotopic in situ hybridization: precise localization of the human type II collagen gene (COL2A1). Hum Genet 86: 14–16.
Traut, W., Eickhoff, U. and Schorch, J.-C. 2001. Identification and analysis of sex chromosomes by comparative genomic hybridization (CGH). Methods Cell Sci 23: 155–161.
Traut, W. and Winking, H. 2001. Meiotic chromosomes and stages of sex chromosome evolution in fish: zebrafish, platyfish and guppy. Chromosome Res 9: 659–672.
Tsuchiya, K., Wakana, S., Suzuki, H., Hattori, S. and Hayashi, Y. 1989. Taxonomic study of Tokudaia (Rodentia: Muridae): I. Genetic differentiation. Memoirs Natl Sci Museum, Tokyo 22: 227–234.
Uno, Y., Nishida, C., Oshima, Y., Yokoyama, S., Miura, I., Matsuda, Y. and Nakamura, M. 2008. Comparative chromosome mapping of sex-linked genes and identification of sex chromosomal rearrangements in the Japanese wrinkled frog (Rana rugosa, Ranidae) with ZW and XY sex chromosome systems. Chromosome Res 16: 637–647.
Valente, G.T., Schneider, C.H., Gross, M.C., Feldberg, E. and Martins, C. 2009. Comparative cytogenetics of cichlid fishes through genomic in-situ hybridization (GISH) with emphasis on Oreochromis niloticus. Chromosome Res 17: 791–799.
Ventura, K., O’Brien, P.C.M., Yonenaga-Yassuda, Y. and Ferguson-Smith, M.A. 2009. Chromosome homologies of the highly rearranged karyotypes of four Akodon species (Rodentia, Cricetidae) resolved by reciprocal chromosome painting: the evolution of the lowest diploid number in rodents. Chromosome Res 17: 1063–1078.
Wienberg, J. 2004. The evolution of eutherian chromosomes. Curr Opin Genet Dev 14: 657–666.
Yamada, K., Nishida-Umehara, C. and Matsuda, Y. 2002. Characterization and chromosomal distribution of novel satellite DNA sequences of the lesser rhea (Pterocnemia pennata) and the greater rhea (Rhea americana). Chromosome Res 10: 513–523.
Yamada, K., Nishida-Umehara, C. and Matsuda, Y. 2005. Molecular and cytogenetic characterization of site-specific repetitive DNA sequences in the Chinese soft-shelled turtle (Pelodiscus sinensis, Trionychidae). Chromosome Res 13: 33–46.
Yamada, K., Nishida-Umehara, C., Ishijima, J., Murakami, T., Shibusawa, M., Tsuchiya, K., Tsudzuki, M. and Matsuda, Y. 2006. A novel family of repetitive DNA sequences amplified site-specifically on the W chromosomes in neognathous birds. Chromosome Res 14: 613–627.