THE IDENTIFICATION AND CHARACTERIZATION OF MICROSATELLITES IN THE COMPACT GENOME OF THE JAPANESE PUFFERFISH, FUGU RUBRIPES - PERSPECTIVES IN FUNCTIONAL AND COMPARATIVE GENOMIC ANALYSES

Fugu rubripes (Fugu) has one of the smallest recorded vertebrate genom es and is an economic tool for comparative DNA sequence analysis. Init ial characterization of 128 kb of Fugu DNA attributed the compactness of this genome, in part, to a sparseness of repetitive DNA sequence co mpared with mammalian genomic sequences. This payer describes a new an d comprehensive analysis in which 501 theoretically possible microsate llites with a repeat unit of one to six bases were used to query two o rders of magnitude more Fugu DNA (i.e. 11.338 Mb). A total of 6042 mic rosatellites were identified and categorized. In decreasing order, the 20 most frequently occurring microsatellites are AC, A, C, AGG, AG, A GC, AAT, AAAT, ACAG, ACGC, ATCC, AAC, ATC, AGGG, AAAG, AAG, AAAC, AT, CCG and TTAGGG. The 20 most frequently occurring microsatellites repre sent 81.79% of all microsatellites identified. Our results indicate th at one microsatellite occurs every 1.876 kb of DNA in Fugu, 11.55% of the microsatellites are detected in open reading frames that are predi cted protein coding regions. With respect to the proportion of microsa tellites present in open reading frames and the total abundance (bp) o f all microsatellites, the genome of Fugu is similar to the genome of many other vertebrate species. Previous estimates performed indicate t hat approximately 1% of many vertebrate genomes are comprized of micro satellite sequences. However, many differences prevail in the abundanc e and frequency of the individual microsatellite classes. Many of the frequently occurring microsatellites in Fugu are known to code in othe r species for regions in proteins such as transcription factors, whils t others are associated with known functions, such as transcription fa ctor binding sites and form part of promoter regions in DNA sequences of genes. Therefore, it is likely that such repeats in genomes have a role in the evolution of genes, regulation of gene expression and cons equently the evolution of species. (C) 1998 Academic Press Limited.