SIMREP: a program simulating differential DNA replication

During endoreplication, different organisms in different taxa carry out DNA syntheses without nuclear division. The result of such endocycles is either a polyploid nucleus or a polytene architecture of the chromosomes. Since not all sequences of the genome may be reduplicated simultaneously and to the same extent, endocycles provide an opportunity for primary cell differentiation at the DNA level as a result of DNA amplification or underreplication. We have designed a numerical model which simulates differential endoreplications. The program SIMREP is written in TURBO PASCAL 4.0 and can be executed on a PC/XT/AT with MS-DOS greater than or equal to 2.0. It uses diploid DNA contents derived from meiotic or mitotic nuclei together with data on amounts of DNA present after a given number of endocycles. SIMREP can be applied to genomes containing arbitrary numbers of chromosomes (maximum N = 24) to model details of their replication behaviour. It is also useful in analysing differential replication of single genes. The application of SIMREP is illustrated with two examples. (1) Female and male specific types of underreplication were found in the chironomid midge Prodiamesa olivacea. The heterosomes which appear homomorphic in metaphases were identified by their differential polytenization. (2) The Y chromosome of Drosophila nasutoides was assessed to ascertain whether its replication is regulated in parallel with, or independently from the large chromosome pair 4.