Xenopus borealis and Xenopus laevis 28 S ribosomal DNA and the complete 40 S ribosomal precursor RNA coding units of both species

Abstract

We have determined the nucleotide sequence of Xenopus borealis 28S ribosomal DNA (rDNA) and have revised the sequence of Xenopus laevis 28S rDNA (Ware et al., Nucl. Acids Res. 11, 7795-7817 (1983)). In the regions encoding the conserved structural core of 28S rRNA (2490 nucleotides) there are only four differences between the two species, each difference being a base substitution. In the variable regions, also called eukaryotic expansion segments (ca. 1630 nucleotides) there are some 61 differences, due to substitutions, mini-insertions and mini-deletions. Thus, evolutionary divergence in the variable regions has been at least 20-fold more rapid than in the conserved core. A search for intraspecies sequence variation has revealed minimal heterogeneity in X. laevis and none in X. borealis. At three out of four sites where heterogeneity was found in X. laevis (all in variable regions) the minority variant corresponded to the standard form in X. borealis. Intraspecies heterogeneity and interspecies divergence in the 28S variable regions are much less extensive than in the transcribed spacers. The 28S sequences are from the same clones that were used previously for sequencing the 18S genes and transcribed spacers. The complete sequences of the 40S precursor regions of the two reference clones are given.

U17XS8, a small nucleolar RNA with a 12 nt complementarity to 18S rRNA and coded by a sequence repeated in the six introns ofXenopus laevisribosomal protein S8 gene

“…In this structure some of the proposed stems involve particularly well conserved sequences, others involve compensatory changes. As an example, the pairing of the first seven nucleotides at the very 5' end (nt 1-7) with nt 102-108 (nt numbering as in Figure 1) (24) has revealed that it contains a 12 nt sequence which can perfectly pair, allowing one G-U pairing, with Xenopus laevis 18S rRNA. This complementarity, shown in Figure 5, is highly significant in consideration of the small size of the RNA.…”

Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian

“…X79878 (Winnepenninckx et al 1995a); ecdysozoan (spider) Eurypelma (Aphonopelma) californica X13457 (Hendriks et al 1988); crinoids Endoxocrinus parrae, Z80951 (Littlewood et al 1997), and Metacrinus sp., AY275897 (Cohen et al 2004); chordate Xenopus laevis, X59734 (Ajuh et al 1991); sponge Soleniscus radovani, AF452017 (Manuel et al 2003 cf.…”

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

“…These sites could have been caused by nucleotide insertion only in the Xenopus lineage. A previous investigation showed that the 28S rRNA gene of vertebrates had 11 " variable regions" with numerous polymorphic and gap sites between human and Xenopus (Ajuh et al, 1991). When examined under electron microscopic, these regions were thought to correspond to the loop regions in secondary structures of 28S rRNA (Ajuh et al, 1991).…”

“…In amphibians, the nucleotide sequences of the rRNA precursor have been completely clarified in only the two tetraploid species of Xenopus (Ajuh et al, 1991). In the other amphibian species examined, only the short nucleotide sequences of some rDNA fragments have been Edited by Yoko Satta * Corresponding author.…”

“…E-mail: msumida@hiroshima-u.ac.jp determined (Hillis et al, 1993). While the two species of Xenopus share almost identical rRNA coding regions, the ITS regions differ greatly between them (Ajuh et al, 1991). Sequence data are not apt to distinguish speciation events between different ploidy levels, nor do they contain information on the allopolyploidization events themselves (Kobel et al, 1998).…”