Characterization of an A/T-rich family of sequences from channel catfish (Ictalurus punctatus)

A family of highly repetitive DNA sequences referred to as Xba elements was identified and characterized from the channel catfish (Ictalurus punctatus] genome. The Xba elements represent about 5% to 6% of the total genomic DNA of the channel catfish. The Xba elements are distributed specifically in the channel catfish and blue catfish (I. furcatus), but not in closely related species such as white catfish (Ameiurus catus) and flathead catfish (Pylodictus olivaris). These Xba elements are arranged as head-to-tail tandem repeats. Seven sequences were sequenced. They are A/T-rich (over 65%). Each sequence contains four copies of the ATTA repeat and eight copies of (A)(3-6) GT/TG motifs whose function is not known. Each unit of the repeats is 325 bp from the Kansas strain, and 321 pb from the Auburn and Stuttgart strains of channel catfish. The Xba elements are conserved in length within a specific strain, and highly conserved in sequence identity. Sequence identity is more conserved among copies isolated from the same strain than from different strains. The sequence length polymorphism among strains may be useful for identification of strains by polymerase chain reaction analysis. Many features of these elements could make them potentially important for development of homologous recombination expression vectors and position-independent expression vectors.