Sequencing and analysis of the internal transcribed spacers (ITSs) and coding regions in the EcoR I fragment of the ribosomal DNA of the Japanese pond frog Rana nigromaculata

Abstract

The rDNA of eukaryotic organisms is transcribed as the 40S-45S rRNA precursor, and this precursor contains the following segments: 5' -ETS -18S rRNA -ITS 1 -5.8S rRNA -ITS 2 -28S rRNA -3'. In amphibians, the nucleotide sequences of the rRNA precursor have been completely determined in only two species of Xenopus . In the other amphibian species investigated so far, only the short nucleotide sequences of some rDNA fragments have been reported. We obtained a genomic clone containing the rDNA precursor from the Japanese pond frog Rana nigromaculata and analyzed its nucleotide sequence. The cloned genomic fragment was 4,806 bp long and included the 3'-terminus of 18S rRNA, ITS 1, 5.8S rRNA, ITS 2, and a long portion of 28S rRNA. A comparison of nucleotide sequences among Rana , the two species of Xenopus , and human revealed the following: (1) The 3'-terminus of 18S rRNA and the complete 5.8S rRNA were highly conserved among these four taxa. (2) The regions corresponding to the stem and loop of the secondary structure in 28S rRNA were conserved between Xenopus and Rana , but the rate of substitutions in the loop was higher than that in the stem. Many of the human loop regions had large insertions not seen in amphibians. (3) Two ITS regions had highly diverged sequences that made it difficult to compare the sequences not only between human and frogs, but also between Xenopus and Rana . (4) The short tracts in the ITS regions were strictly conserved between the two Xenopus species, and there was a corresponding sequence for Rana . Our data on the nucleotide sequence of the rRNA precursor from the Japanese pond frog Rana nigromaculata were used to examine the potential usefulness of the rRNA genes and ITS regions for evolutionary studies on frogs, because the rRNA precursor contains both highly conserved regions and rapidly evolving regions.

Species composition of the genus Saprolegnia in fin fish aquaculture environments, as determined by nucleotide sequence analysis of the nuclear rDNA ITS regions

“…The utility of nrDNA genes for phylogenetic studies has been well demonstrated for many taxa (Baldwin 1992;Gardes & Bruns 1993;Chen et al 2000Chen et al , 2001Sumida et al 2004;Li et al 2005;Ma & Xu 2005), including oomycetes (Cooke & Duncan 1997;Schena & Cooke 2006). The combination of highly conserved coding regions (18S, 5.8S, and 28S) separated by the variable, non-coding ITS regions has provided a useful resource for taxonomic and phylogenetic studies (Long & Dawid 1980;Richard et al 2008), allowing resolution of many taxa down to the family or genus level (Oditmann et al 2004;Ballesteros et al 2007), especially when morphological traits were incorporated into the analysis (Molina et al 1995;Chen et al 2000Chen et al , 2001Hulvey et al 2007;Johnson et al 2008;Ke et al 2009).…”

Effects of permissible maximum-contamination levels of VOC mixture in water on total DNA, antioxidant gene expression, and sequences of ribosomal DNA of Drosophila melanogaster

“…The ribosomal DNA is a DNA sequence assembled from the external transcribed spacer (ETS) and the 18S, ITS1, 5.8S, ITS2, and 28S units. Coding in the 18S and 28S regions are known to be conserved (Paques et al 1995), but the ITS regions are variable because of bearing insertions, deletions, and point-mutation sources from environmental signals (Sumida et al 2004). Currently, hundreds of genes are known to be responsible for environmental stress defence mechanisms in Eukaryotic genomic DNA, and many have assigned functions in the stress response (Loar et al 2004).…”

It’s okay to be green: Draft genome of the North American bullfrog (Rana [Lithobates] catesbeiana)

“…The genomes of two Xenopus species (X. tropicalis and X. laevis) have been sequenced and annotated to some extent (Buisine, et al, 2015;Session, et al, 2016), but these pipids have an estimated divergence from the Ranidae ~260 million years ago (Sumida, et al, 2004). This evolutionary separation is accentuated by their differing life histories, behavior, markedly different sex differentiation systems (Eggert, 2004); and recent evidence suggests that the innate immune system of Xenopus is fundamentally different from three frog families including the Ranidae (Kiemnec-Tyburczy, et al, 2012).…”