Genomic analysis of the vitellogenin locus in rainbow trout (Oncorhynchus mykiss) reveals a complex history of gene amplification and retroposon activity

Vitellogenins (Vtg) are the major yolk proteins in most oviparous organisms . They are encoded by a small number of genes - between one and four depend ing on the species. Characterization of the Vtg region in the genome of the rainbow trout reveals unusual features, however, in that this locus contai ns twenty complete genes and ten pseudogenes per haploid genome. The Vtg ge nes differ from each other by insertion, deletion and rearrangement events, although, at the sequence level, they show a high degree of similarity. Fl uorescent in situ hybridization (FISH), pulsed-field gel electrophoresis (P FGE) and Southern analysis indicate that all gene copies are contained in a . single 1500-kb region, and that most of the genes form tandem arrays sepa rated by a conserved 4.5-kb intergenic region. The presence of large reiter ated fragments indicates that this region has been subjected to several amp lification events. The presence of a retroposon element (called I9) in Vtg intron 9 appears to be responsible for the silencing of at least nine of th e ten pseudogenes. Two other incomplete retrotransposons (one LTR- and one LINE-type) and sequences derived from a HIV-like retrovirus are inserted in to the conserved intergenic region, very close to the transcription start s ite. Their presence in all Vtg 5'-flanking regions suggests a possible role in gene amplification at this locus.