The nucleotide sequences of 5S rRNAs from a rotifer, Brachionus plicatilis, and two nematodes, Rhabditis tokai and Caenorhabditis elegans

A new set of highly efficient primers for COI amplification in rotifers

Rotifers are a small-sized but key group of freshwater zooplankters with high species richness, linking primary producers to higher consumers in aquatic food webs. DNA barcoding has been widely used in exploring its biodiversity, cryptic speciation and phylogeny. However, the inefficiency of universal primers to amplify COI of rotifers hinders our understanding of their species richness and genetic diversity. Here, we develop a new pair of primers, 30 F and 885 R, to amplify the COI gene of rotifers. We used 22 species to test their PCR success rate and found that the new pair of primers was more efficient (86%) than two pairs of universal primers, namely, dgLCO and dgHCO (32%), and Folmer primers (59%). The new primers will allow the barcoding of groups that were so far difficult to sequence and will contribute to clarify species diversity and phylogeny of rotifers.

A trans-spliced leader RNA sequence in plant parasitic nematodes

A trans-spliced leader gene has been identified in the genomes of the potato cyst nematodes Globodera rostochiensis and G. pallida. The gene contains a 22-nt sequence identical to that of the leader sequence of Caenorhabditis elegans, a consensus splice donor site and a putative Sm antigen binding site. In common with other nematodes the spliced leader gene is present in tandem repeating units together with the 5S ribosomal RNA gene. Variation in the length of the intergenic spacer region has permitted the design of polymerase chain reaction primers which can be used to reveal repeat length variants diagnostic for G. rostochiensis and G. pallida and the Pa1 pathotype of G. pallida.

Evolution of multicellular animals as deduced from 5S rRNA sequences: a possible early emergence of the Mesozoa

The nucleotide sequences of 5S rRNA from a mesozoan Dicyema misakiense and three metazoan species, i.e., an acorn-worm Saccoglossus kowalevskii, a moss-animal Bugula neritina, and an octopus Octopus vulgaris have been determined. A phylogenic tree of multicellular animals has been constructed from 73 5S rRNA sequences available at present including those from the above four sequences. The tree suggests that the mesozoan is the most ancient multicellular animal identified so far, its emergence time being almost the same as that of flagellated or ciliated protozoans. The branching points of planarians and nematodes are a little later than that of the mesozoan but are clearly earlier than other metazoan groups including sponges and jellyfishes. Many metazoan groups seem to have diverged within a relatively short period.

Two 5S genes are expressed in chicken somatic cells

Two 5S RNA species were detected in chicken cells. 5S I RNA has the nucleotide sequence of chicken 5S RNA previously published by Brownlee et al. (1) and 5S II RNA differs from it by 10 mutations. The secondary structure of both species is compatible with that proposed for other eukaryotic 5S RNAs. 5S II RNA represents 50-60% of 5S I RNA. Both species were found in total chicken liver and brain and were present in polysomes in the same relative proportions. Only one 5S RNA species could be detected in rat liver and HeLa cells. Chicken is the first vertebrate described so far in which two 5S RNA genes are expressed in somatic cells.

The nucleotide sequences of 5S rRNAs from two ribbon worms: Emplectonema gracile contains two 5S rRNA species differing considerably in their sequences

The nucleotide sequences of 5S rRNAs from two nemerteans (ribbon worms), Lineus geniculatus and Emplectonema gracile have been determined. Emplectonema has two 5S rRNA species that are composed of 119 and 120 nucleotides, respectively. The sequences of these two 5S rRNAs differ at 22 positions. On the other hand, only a single 5S rRNA species was found in Lineus. The sequence similarity percents are 88% (Lineus/Emplectonema longer 5S rRNA), 82% (Emplectonema longer/Emplectonema shorter) and 80% (Lineus/Emplectonema shorter). The comparisons of these sequences with those of other organisms suggest that the phylum Nemertinea is most related to the Mollusca (91%) and the Rotifera (89%), but not to fresh-water planarias (72%).

The nucleotide sequences of 5S rRNAs from a sea-cucumber, a starfish and a sea-urchin

The nucleotide sequences of 5S rRNA from three echinoderms, a sea-cucumber Stichopus oshimae, a starfish Asterina pectinifera and a sea-urchin Hemicentrotus pulcherrimus have been determined. These 5S rRNAs are all 120 nucleotides long. The echinoderm sequences are more related to the sequences of proterostomes animals such as mollusc, annelids and some others (87% identity on average) than to those of vertebrates (82% identity on average).

The nucleotide sequences of the 5S rRNAs of four mushrooms and their use in studying the phylogenetic position of basidiomycetes among the eukaryotes

The nucleotide sequences of the 5 S ribosomal RNAs of the mushrooms Russula cyanoxantha, Pleurotus ostreatus, Agaricus edulis, and Auricularia auricula-judae were determined. The sequences fit in a universal five-helix secondary structure model for 5 S RNA. As in most other 5 S RNAs, some helical areas contain non-standard base pairs. A clustering method was used to reconstruct an evolutionary tree from 82 eukaryotic 5 S RNA sequences. It allows to make a choice between alternative systematic classifications for basidiomycetes and reveals that the fungal kingdom is highly polyphyletic.

Nucleotide sequence of 5 S rRNA from gonads of a Japanese ascidian, Holocynthia roretzi

The nucleotide sequence of 5 S rRNa from gonads of an ascidian Holocynthia roretzi has been determined. The sequence is almost equally related to those of vertebrates and most of the multicellular animal groups. The secondary structure of this 5 S rRNA fits in with the general structural model for multicellular 5 S rRNA.

Nucleotide sequences of 5s rRNAs from sponge Halichondria japonica and tunicate Halocynthia roretzi and their phylogenetic positions

The nucleotide sequences of 5S rRNAs from sponge Halichondria japonica and tunicate Halocynthia roretzi were determined by chemical and enzymatic gel methods. Their phylogenetic positions among metazoans were derived from the 5S rRNA sequences by a computer analysis based on the maximum parsimony principle. It was suggested that the sponge is closely related to several invertebrates and the tunicate has affinity to vertebrates rather than invertebrates.