Genomic nucleotide variation in the ITS1 rDNA spacer of land snails

Abstract

Ribosomal RNA is coded by the rDNA gene cluster. Hundreds of rDNA loci are consecutively arranged and form repeated motifs on chromosomes. The Internal Transcribed Spacer 1 (ITS1) is part of the eukaryotic rDNA locus. This spacer is a relatively fast evolving, ‘non-coding’ element. It is often used in phylogenetic reconstructions of closely related taxa. The ITS1 separates two functional regions: the 18S rDNA and the 5.8S rDNA (Fig. 1). There are usually no or very few ITS1 nucleotide polymorphisms within an animal species (0–3% intraspecific variation1–4). The phenomenon of very low intraspecific rDNA variation is explained by the concept of concerted evolution in the gene pool of a species under molecular drive.5–7 Yet, there are exceptions from the rule of very low intraspecific rDNA variation, particularly in crustaceans8 and in some species-flocks. For example, in the Cicindela dorsalis complex (tiger beetle), in the Simulium damnosum group (West African black flies), in corals with reticulate evolution and in a few plant species the genomic variation in the ITS1 is extremely high, with some sequences showing as much as 20–35% intraspecific divergence.9–12 In the following contribution, we analyse the extent of ITS1 variation of four taxonomically robust species of land snail of different family categories, i.e. within Acanthinula aculeata (Valloniidae sensu lato), Arianta arbustorum (Helicoidea), Cochlodina fimbriata (Clausiliidae), and Vallonia costata (Valloniidae sensu stricto). We show that one species (A. aculeata) exhibits a high level of ITS1 variation, whilst another species (V. costata) displays nearly no variation. The other two taxa display moderate variation. We also examine the ITS1 rDNA for highly conserved sequence motifs and investigate the extent of nucleotide variation within such motifs. Evolutionarily conserved regions in ribosomal spacers are suspected to be involved in the maturation of the precursor rRNA.13–15 Finally, we discuss the possible occurrence of rDNA pseudogenes in PCR amplicons and genome databases.