Fluorescent in situ hybridization and characterization of the SalI family of satellite repeats in the Haliotis L. species (abalone) of the Northeast Pacific

The SalI satellite repeat previously identified in Haliotis L. (abalone) was thought to be present in H, rufescens and absent in H. fulgens. However, we show here that SalI is also found in H. fulgens and is not useful for screening hybrid individuals bred in aquaculture or occurring naturally in the wild. Still is a family of predominantly subtelomeric tandemly repeated sequences, and sequenced clones revealed clustering to species and little intraspecific variation. Analysis of SalI sequence divergence between Haliotis species of the Northeast Pacific revealed that evolutionary distances correlate well with bathymetric and latitudinal species distributions. Analysis of the structure of the tandem repeats revealed two re,,ions of high sequence conservation that may contain conserved transcription factor binding sites, a surprise for an apparently non-coding tandem repeat. We speculate that these regions might be involved in heterochromatin silencing, perhaps mediated via transcriptional activity and RNA interference. The repeats show substantial differences in their chromosomal distributions. even between individuals of the same species, indicating a dynamic organization of repeats, perhaps mediated via sequence homogenization.