Summary
DNA preparations obtained from 122 species of fishes, 5 species of amphibians, and 13 species of reptiles were investigated in their compositional properties by analytical equilibrium centrifugation in CsCl density gradients. These species represented 21 orders of Osteichthyes, 3 orders of Chondrichthyes, 2 orders of amphibians, and 3 orders of reptiles. Modal buoyant densities of fish DNAs ranged from 1.696 to 1.707 g/cm3, the vast majority of values falling, however, between 1.699 and 1.704 g/cm3, which is the range covered by the DNAs of amphibians and reptiles. In all cases, DNA bands in CsCl were only weakly asymmetrical and only very rarely were accompanied by separate satellite bands (mostly on the GC-rich side). Intermolecular compositional heterogeneities were low in the vast majority of cases, and, like CsCl band asymmetries, at least partially due to cryptic or poorly resolved satellites. The present findings indicate, therefore, that DNAs from cold-blooded vertebrates are characterized by a number of common properties, namely a very wide spectrum of modal buoyant densities, low intermolecular compositional heterogeneities, low CsCl band asymmetries, and, in most cases, small amounts of satellite DNAs. In the case of fish DNAs a negative correlation was found between the GC level and the haploid size (c value) of the genome. If polyploidization is neglected, this phenomenon appears to be mainly due to the fact that increases and decreases in GC are associated with contraction and expansion phenomena, respectively, of intergenic noncoding sequences, which are GC poor relative to coding sequences.
Similar content being viewed by others
References
Allendorf FW, Thorgaard GH (1984) In: Turner BJ (ed) Evolutionary genetics of fishes. Plenum, New York, pp 1–45
Alvarez MC, Cano J, Thode G (1980) DNA content and chromosome complement ofChromis chromis (Pomacentridae, Perciformes). Caryologia 33:267–274
Bernardi G (1971) Chromatography of nucleic acids on hydroxyapatite columns. In: Grossman L, Moldave K (eds) Methods in enzymology, vol 21. Academic Press, New York, pp 95–139
Bernardi G (1989) The isochore organization of the human genome. Annu Rev Genet 23:637–661
Bernardi G, Bernardi G (1985) Codon usage and genome composition. J Mol Evol 22:363–365
Bernardi G, Bernardi G (1986) Compositional constraints and genome evolution. J Mol Evol 24:1–11
Bernardi G, Bernardi G (1990) Compositional transitions in the nuclear genomes of cold-blooded vertebrates. J Mol Evol 31:282–293
Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F (1985) The mosaic genome of the vertebrates. Science 228:953–958
Bernardi G, Pizon V, Cuny G, Haschemeyer AEV, Bernardi G (1986) AND et taxonomie des poissons. Oceanis 12:377–380
Bernardi G, Mouchiroud D, Gautier C, Bernardi G (1988) Compositional patterns in vertebrate genomes: conservation and change in evolution. J Mol Evol 28:7–18
Birstein VJ (1982) Structural characteristics of genome organization in amphibians: differential staining of chromosomes and DNA structure. J Mol Evol 18:73–91
Birstein VJ, Vassiliev VP (1987) Tetraploid-octoploid relationships and karyological evolution in the order Acipenseriformes (Pisces). Genetica 72:3–12
Cano J, Thode G, Alvarez MC (1982) Karyoevolutive considerations in 29 Mediterranean teleost fishes. Vie Milieu 32: 21–24
Corneo G, Ginelli E, Soave C, Bernardi G (1968) Isolation and characterization of mouse and guinea pig satellite DNAs. Biochemistry 7:4373–4379
Cortadas J, Macaya G, Bernardi G (1977) An analysis of the bovine genome by density gradient centrifugation: fractionation in Cs2SO4/3,6 bis(acetato-mercurimethyl)dioxane density gradient. Eur J Biochem 76:13–19
Cortadas J, Olofsson B, Meunier-Rotival M, Macaya G, Bernardi G (1979) The DNA components of the chicken genome. Eur J Biochem 99:179–186
Cuny G, Soriano P, Macaya G, Bernardi G (1981) The major components of the mouse and human genomes: preparation, basic properties, and compositional heterogeneity. Eur J Biochem 111:227–233
De Lucca FL, Imaizumi M, Haddad A (1974) Characterization of ribonucleic acids from the venom glands ofCrotalus durissus terrificus (Ophidia, Reptilia) after manual extraction of the venom. Biochem J 139:151–156
Eigner J, Doty P (1965) The native, denatured and renatured states of deoxyribonucleic acid. J Mol Biol 12:549–580
Felix K, Jilke I, Zahn RK (1956) Die Deoxyribonucleinsaure Einiger Fischspermien. Hoppe Seyler's Z Physiol Chem 303:140–152
Filipski J, Thiery JP, Bernardi G (1973) An analysis of the bovine genome by Cs2SO4/Ag+ density gradient centrifugation. J Mol Biol 80:177–197
Gold JL, Karel WJ (1988) DNA base composition and nucleotide distribution among fifteen species of teleostan fishes. Comp Biochem Physiol 90B:715–719
Gosline WA (1970) A reinterpretation of the fish order Gobiesociformes. Proc Calif Acad Sci, Ser 4 37:363–382
Hinegardner R (1976) The cellular DNA content of sharks, rays and some other fishes. Comp Biochem Physiol B55:367–370
Hinegardner R, Rosen DE (1972) Cellular DNA content in the evolution of teleostan fishes. Am Nat 106:621–644
Hudson AP, Cuny G, Cortadas J, Haschemeyer AEV, Bernardi G (1980) An analysis of fish genomes by density gradient centrifugation. Eur J Biochem 112:203–210
Hummel S, Meyerhof W, Korge E, Knöchel W (1984) Characterization of highly and moderately repetitive 500 bp EcoRI fragments fromXenopus laevis DNA. Nucleic Acids Res 12:4921–4938
Ifft JB, Voet DM, Vinograd J (1961) The determination of density distributions and density gradients in binary solutions at equilibrium in the ultracentrifuge. J Phys Chem 65:1138–1145
Karel WJ, Gold JL (1987) A thermal denaturation study of genome DNAs from North-American minnows (Cyprinidae, Teoleostei). Genetica 74:181–187
Kay ERM, Simmons NS, Dounce AL (1952) An improved preparation of sodium desoxyribonucleate. J Am Chem Soc 74:1724–1726
Kornfield I (1984) In: Turner BJ (ed) Evolutionary genetics of fishes. Plenum, New York, pp 591–616
Macaya G, Thiery JP, Bernardi G (1976) An approach to the organization of eukaryotic genomes at a macromolecular level. J Mol Biol 108:237–254
Majumdar KC, McAndrew BJ (1986) Relative DNA content of somatic nuclei and chromosomal studies in three genera,Tilapia, Sarotherodon, andOreochromis of the tribe Tilapiini (Pisces, Cichlidae). Genetica 68:175–188
Matsuura K (1979) Phylogeny of the superfamily Balistoidea (Pisces, Tetraodontiformes). Mem Fac Fish Hokkaido University 26:49–169
Medrano L, Bernardi G, Couturier J, Dutrillaux B, Bernardi G (1988) Chromosome banding and genome compartmentalization in fishes. Chromosoma 96:178–183
Morescalchi A, Olmo E (1982) Single-copy DNA and vertebrate phylogeny. Cytogenet Cell Genet 34:93–101
Mouchiroud D, Fichant G, Bernardi G (1987) Compositional compartmentalization and gene composition in the genomes of vertebrates. J Mol Evol 26:198–204
Mouchiroud D, Gautier C, Bernardi G (1988) The compositional distribution of coding sequences and DNA molecules in humans and murids. J Mol Evol 27:311–320
Nelson JS (1984) Fishes of the world, ed 2. Wiley, New York
Ohno S, Atkins NB (1966) Comparative DNA values and chromosome complements of right species of fishes. Chromosoma 18:455–466
Olmo E (1981) Evolution of genome size and DNA base composition in reptiles. Genetica 57:39–50
Olmo E, Stingo V, Cobror O, Capriglione T, Odierna G (1982) Repetitive DNA and polyploidy in selachians. Comp Biochem Physiol 73B:739–745
Olmo E, Capriglione T, Odierna G (1989) Genome size evolution in vertebrates: trends and constraints. Comp Biochem Physiol 92B:447–453
Olofsson B, Bernardi G (1983) Organization of nucleotide sequences in the chicken genome. Eur J Biochem 130:241–245
Pedersen RA (1971) DNA content, ribosomal gene multiplicity and cell size in fishes. J Exp Zool 177:65–78
Perrin P, Bernardi G (1987) Directional fixation of mutations in vertebrate evolution. J Mol Evol 26:301–310
Pizon V (1983) Organisation des séquences nucléotidiques dans les génomes de poissons. Thèse de 3è cycle, Université Paris VI
Pizon V, Cuny G, Bernardi G (1984) Nucleotide sequence organization in the very small genome of a tetraodontid fish,Arothron diadematus. Eur J Biochem 140:25–30
Prunell A, Bernardi G (1973) Fractionation of native and denatured DNA on agarose columns. J Biol Chem 248:3433–3440
Rasch EM, Darnell RM, Kallman KD, Abramoff P (1965) Cytophotometric evidence for triploidy in hybrids of the gynogenetic fish,Poecilia formosa. J Exp Zool 160:155–169
Salinas J, Zerial M, Filipski J, Bernardi G (1986) Gene distribution and nucleotide sequence organization in the mouse genome. Eur J Biochem 106:469–478
Schildkraut CL, Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl. J Mol Biol 4:430–443
Schmid CW, Hearst JE (1972) Sedimentation equilibrium of DNA samples heterogeneous in density. Biopolymers 11:1913–1918
Schmid M, Guttenbach M (1988) Evolutionary diversity of reverse (R) fluorescent chromosome bands in vertebrates. Chromosoma 97:101–114
Schwartz FJ, Maddock MB (1986) Comparisons of karyotypes and cellular DNA contents within and between major lines of elasmobranchs. In: Uyeno T, Arai R, Taniuchi T, Matsuura K (eds) Indo-Pacific fish biology. Ichthyological Society of Japan, Tokyo, pp 148–157
Sober HA (ed) (1970) Handbooks of biochemistry. CRC Press, Cleveland OH, p H-109
Stingo V (1986) Correlazioni tra quantità di DNA totale e DNA DAPI-positivo in Teleostei e Selaci. Basic Appl Histochem [Suppl] 30:164
Stingo V, Du Buit MH, Odierna G (1980) Genome size of some selachian fishes. Bol Zool 47:129–137
Stingo V, Capriglione T, Rocco L, Improta R, Morescalchi (1989) Genome size and A-T rich DNA in selachians. Genetica 79: 197–205
Szybalski W (1968) Use of cesium sulfate for equilibrium density gradient centrifugation. In: Grossmann L, Moldave K (eds) Methods in enzymology, part B, vol 12. Academic Press, New York, pp 330–360
Thiery JP, Macaya G, Bernardi G (1976) An analysis of eukaryotic genomes by density gradient centrifugation. J Mol Biol 108:219–235
Thompson KW (1976) Some aspects of chromosome evolution of the Cychlidae (Teleostei, Perciformes) with emphasis on neotropical forms. Ph.D. dissertation, University of Texas, Austin, Texas
Zerial M, Salinas J, Filipski J, Bernardi G (1986) Gene distribution and nucleotide sequence organization in the human genome. Eur J Biochem 160:479–485
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Bernardi, G., Bernardi, G. Compositional patterns in the nuclear genome of cold-blooded vertebrates. J Mol Evol 31, 265–281 (1990). https://doi.org/10.1007/BF02101122
Received:
Revised:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF02101122