Chromosome Research I993, 1, 77-86 Organization and molecular cytogenetics of a satellite DNA family from Hoplias malabaricus (Pisces, Erythrinidae) Thomas Haaf, Michael Schmid, Claus Steinlein, Pedro M. Galetti, Jr, & Huntington F. Willard Received 17 February 1993; received in revised form 1 April 1993; Accepted for publication by R. Baker 1 April 1993 The chromosomes of the primitive South American teleost fish Hoplias malabaricus have been analyzed by classical cytogenetic (C-, AgNOR-, Hoechst 33258-, and Q-banding) techniques. A highly repetitive DNA family has been cloned and sequenced. It is a tandemly re- peated sequence of about 355 bp, yielding an overall base pair composition of 67% AT with long runs of >50% As and 70% Ts. Analysis of sequence variation has allowed the further categorization of Hoplias satellite DNA into two evolutionarily related subfamilies A and B, distinguishable by characteristic insertions and deletions within this 355-bp monomer. Subfamily A satellite is found (in diverged form) at the centromeres of most H. malabaricus chromosomes. Sequence variants are clustered on specific chromosomal subsets. Subfamily B satellite is highly specific for the paracentromeric heterochromatin on one particular chromosome pair by fluorescence in situ hybridization. These results indicate that the Hoplias satellite DNA family has evolved in a concerted manner predomin- antly via recombination events involving homologous, rather than non-homologous chromosome regions. The clones isolated here may be useful for the molecular, genetic, and cytological analysis of the genus Hoplias. Key words: centromere, concerted evolution, fish cyto- genetics, Hoplias, satellite DNA Introduction The genomes of higher eukaryotes contain various amounts of non-coding satellite DNA sequences located primarily in the (peri)centromeric regions and less frequently in telomeric and interstitial (heterochromatic) regions of metaphase chro- mosomes. A certain amount of satellite-like repetitive DNA sequences appear to be essential for structural functions at the chromosomal and nuclear level (Singer 1982, Miklos 1985, Haaf and Schmid 1991). Transfection experiments have suggested a role for :c-satellite DNA, the centromeric satellite of primate chromosomes, in centromere function (Haaf et aI. 1992). Satellite DNA sequences are also believed to be a driving force in chromosomal evolution and have been implicated in speciation (Wichman et aI. 1991). The monomeric repeat units of different satellite DNA families vary in length from a few base pairs to several hundred nucleotides (Singer 1982, Miklos 1985). In addition, a high degree of sequence divergence of the order of some 10% can exist between monomers of one satellite DNA family within and between (closely related) species. This is, for example, the case with primate :c-satellite, one of the most thoroughly studied satellite DNA families. At a second level of hierarchy, sequence variants of :c-satellite DNA are organized in tandem arrays that constitute chromosome- specific subsets with clearly definable higher-order repeat units. This (chromosomal) distribution is thought to reflect a concerted mode of sequence evolution among homolo- gous chromosomes (Willard and Waye 1987, Willard 1991). In contrast, sequence variants appear to be completely randomly distributed within Tenebrio molitor satellite DNA (Plohl et al. 1992), possibly suggesting that, in this case, the process of interchromosomal spreading is faster than the mutation rate and/or intrachromosomal homogenization. Indeed, some satellite DNA families, i.e. Drosophila rnelanogaster and feline satellites, show only low levels of sequence variation between < 1% and 3% (Lohe and Brutlag 1986, Fanning 1987), indicating a high rate of homogeni- zation among different (non-homologous) chromosomes. Satellite DNAs have been extensively studied in in- vertebrates and mammals (Singer 1982, Miklos 1985). Corn- T. Haaf (corresponding author) and H. F. Willard were at the Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. M. Schmid and C. Steinlein are at the Department of Human Genetics, W~rzburg University School of Medicine, 8700 W~rzburg, Germany. P.M. Galetti Jr is at the Department of Genetics and Evolution, Federal University of S~o Carlos, I3.560 S~o Carlos, S~o Paulo, Brazil. The present address of H. F. Willard is Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA. Address correspondence to T. Haafi Department of Genetics, 1-147 SHM, 333 Cedar SL PO Box 3333, New Haven, CT 06510-8005, USA. Fax: (q-I) 203 785 7023. 1993 Rapid Communications of Oxford Ltd Chromosome Research Vol 1 1993 77