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Intervening sequences in the ribosomal RNA genes of Ascaris lumbricoides: DNA sequences at junctions and genomic organization.

An rDNA size class in the genome of the nematode Ascaris lumbricoides is described which is interrupted by a 4.5‐kb long intervening sequence located in the 26S coding region. This molecular form occurs in approximately 15 copies per haploid genome and amounts to approximately 5% of the total nuclear rDNA. Intervening sequences are present only in the 8.8‐kb rDNA, but not in the 8.4‐kb rDNA repeating units of A. lumbricoides. Cloning of the interrupted rDNA units revealed, in addition to the main 4.5‐kb insertion, shorter intervening sequences of 4‐kb and 119‐bp length. Both shorter rDNA forms are present in the single copy range of the haploid genome. Sequence analyses of the intervening sequence/rDNA junctions show an identical right‐hand junction for all of the three different rDNA forms. The two shorter intervening sequences are a coterminal subset of the right‐hand end of the main 4.5‐kb insertion, whereas all three insertions have a different left‐hand junction with the coding region of rDNA. Each intervening sequence is flanked by a short direct repeat of variable length, being only once present in the uninterrupted rDNA. The intervening sequences of A. lumbricoides show striking similarity to the organization of type I insertion family in dipteran flies, even though they are inserted at different positions in the 26S coding region. Additional rDNA intervening sequences may be present outside of the rDNA cluster, but in not more than 15‐20 homologous copies per haploid genome.