The 5S ribosomal RNA intergenic region of parasitic nematodes: variation in size and presence of SL1 RNA

Ribosomal RNA (rRNA) sequences have been used extensively as model genes for phylogenetic inference and microbial speciation. Although the small ( similar to 115 bp) gene encoding 5S rRNA in nematodes is extremely conserved, the intergenic region between repeating 5S rRNA coding regions appears to vary greatly in size and nucleotide composition. Furthermore, in many nematode species the locus for the similar to 115 bp spliced leader (SL) RNA involved in trans-splicing of nematode pre-messenger RNA is also found in this 5S rRNA spacer region. The organization of the 5S rRNA gene has been studied in detail in Caenorhabditis elegans, Brugia malayi and Ascaris lumbricoides. In C. elegans the transcriptional orientation of the SL1 RNA gene is opposite to that of 5S rRNA, whereas in Ascaris and filarial species both genes are located on the same strand. Given this apparent variation in overall length and presence of the SL locus within the 5S rRNA spacer, we therefore undertook a systematic survey of the distribution of these characteristics in a broad range of nematode species, with an emphasis on zooparasitic nematodes.