Chromosome Research 1995, 3, 175-181 Identification of highly conserved loci by genome painting Timothy W. Houseal, Joseph A. Cook, William S. Modi & David W. Hale Received 18 August 1994; received in revised form 7 October 1994 Accepted for publication by J. S. (Pat) Heslop-Harrison 7 October 1994 Fluorescence in situ hybridization was used to identify patterns of DNA similarity among the genomes of several rodent taxa. Total genomic or Cot-1 DNAs were used as hybridization probes against metaphase preparations across different taxonomic levels, includ- ing three species of Microfus (suborder Sciurognathi), Mus musculus (suborder Sciurognathi) and Ctenomys steinbachi (suborder Hystricognathi). The hybridiza- tion patterns of Mus or Peromyscus (sciurognath) DNA to Mus metaphases, which were consistent with what is known of the satellite sequences in these species, demonstrated the efficacy of this approach for mole- cular cytogenetics and evolutionary biology. Addi- tional hybridizations to chromosomes of Ctenomys or Microtus identified loci consisting of highly con- served DNA sequences. This approach has proved useful in investigating genome homologies across di- vergent rodent lineages. Chromosome microdissec- tion can be used to characterize these regions further. Key words: fluorescence in situ hybridization, genomic DNA, molecular evolution, repetitive DNA, rodent Introduction Repetitive DNA sequences are ubiquitous in eukaryotic genomes. These sequences are non-randomly distrib- uted both spatially and temporally, and characteriza- tion of these sequences is important in understanding genome organization and evolution. DNA-DNA hy- bridization studies have exploited variations in the reassociation kinetics of these sequences to investigate the systematics and evolution of a number of inverte- brate and vertebrate organisms (Sheldon & Bledsoe 1989 and references therein). While these studies have proved very useful in quantifying genome complemen- tarity, they do not provide information concerning the genomic distribution and organization of these con- served sequences. Fluorescence in situ hybridization (FISH) has recently emerged as a promising tool for studying genome organization and evolution. Hybridizations with total genomic DNA have been used to study the organiza- tion of constituent genomes in human-hamster hybrid pronuclei (Brandriff et al. 1991), plant hybrids (Schwar- zacher et al. 1989, Leitch et al. 1990, 1991, f~rgaard & Heslop-Harrison 1994) and allopolyploid plants (Ben- nett et al. 1992). Studies of genome and/or chromoso- mal evolution have also benefited from various applications of FISH. These investigations, however, have been limited to previously characterized probes, such as those for satellite DNA (Hamilton et al. 1990), ribosomal loci (Brown et al. 1993), transposable ele- ments (Baker & Wichman 1990) or alphoid repeats (Baldini et al. 1991). Additionally, chromosome-specific DNA libraries have been used in various chromosome painting schemes to explore chromosomal evolution among mammals (Wienberg et al. 1990, 1992, Scherthan et al. 1994). We have used high-stringency FISH with total genomic DNA to paint complementary regions among genomes of divergent rodent taxa. Eukaryotic genomic DNAs are enriched for repetitive sequences and provide a convenient source of probe material. This genome painting scheme can be used to explore gen- ome organization and evolution at many taxonomic levels. Our samples (Table 1) represent three highly diverse and chromosomally variable rodent clades following the taxonomy of Wilson & Reeders (1993). Two of these groups, voles (genus Microtus, suborder Sciurognathi) and tuco-tucos (genus Ctenomys, suborder Hystrico- gnathi), were considered by Reig (1989) to be among T.W. Houseal (corresponding author) is at Integrated Genetics, One Mountain Road, Framingham, MA 01701-9322, USA. Tel: (+1) 508 872 8400 extn. 2269; Fax: (+1) 508 6201203. J. A. Cook is at University of Alaska Fairbanks, Fairbanks, AK 99775-1200, USA. W. S. Modi is at Biological Carcinogenesis Development Program, Program Resources, Inc./DynCorp, National Cancer Institute, Frederick Cancer Research and Development Center, Frederick, MD 21702-1201, USA. D.W. Hale is at Department of Biology, Yale University, New Haven, CT 06520-8104, USA. © 1995 Rapid Communications of Oxford Ltd Chromosome Research Vol 3 1995 175