Variability of Nucleotide Sequences in the ITS1–5.8S rRNA–ITS2a–2S rRNA–ITS2 Region of rRNA Gene Cluster in Species of the Family Chironomidae

Abstract

The variability of nucleotide sequences of ribosomal genes and internal transcribed spacers located in the ITS1–5.8S rRNA–ITS2a–2S rRNA–ITS2 region separating the 18S and 28S rRNA genes in the rRNA gene cluster was studied in order to estimate the possibility of using these sequences as molecular markers for species identification and reconstruction of the phylogeny of the family Chironomidae. It was established that, in species of the family Chironomidae, the content of AT base pairs in the sequences of the 5.8S rRNA and 2S rRNA genes is lower (50–57%) than in the sequences of the ITS1, ITS2a, and ITS2 transcribed spacers (64–71%). The sizes of nucleotide sequences of the 5.8S rRNA (123 bp) and 2S rRNA (30 bp) genes in species of the family Chironomidae are conservative, while the sizes of the ITS1, ITS2a, and ITS2 internal transcribed spacers vary both within the species and between species. Neither intraspecific, nor interspecific, nor intergeneric nucleotide differences were found in the sequences of the 2S rRNA gene in 27 species from five genera of the family Chironomidae. Nucleotide sequences of the 5.8S rRNA gene are identical in most studied species of the Chironomus genus. Fixed interspecific nucleotide substitutions were found only in two sites of this gene sequence in three species: C. piger, C. riparius (473С>T), and C. annularius (474A>G). The number of insertions, deletions, and nucleotide substitutions in the sequences of the ITS1, ITS2a, and ITS2 internal transcribed spacers and the whole ITS1–5.8S rRNA–ITS2a–2S rRNA–ITS2 region is generally low within species and increases 5–6 times in sibling species and more than 10 times in morphologically distinct species; that is, it increases in accordance with the growth of taxonomic status of species from the family Chironomidae. The data obtained indicate that nucleotide sequences of ribosomal genes and internal transcribed spacers from the ITS1–5.8S rRNA–ITS2a–2S rRNA–ITS2 region of the rRNA gene cluster can be used as molecular markers for species identification and reconstruction of the phylogeny of the family Chironomidae.