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%).     

Metameric organisation of the nervous system in developmental stages of Urechis caupo (Echiura) and its phylogenetic implications

The phylogenetic position of Echiura is still in continuous debate. The commonly accepted view regards Echiura as a distinct taxon, often classified as phylum, which forms the sister group of the Articulata. The alternative view considers Echiura to be a subtaxon of Annelida, which is supported by numerous shared characters. The correct systematic position of Echiura is inevitably linked to the presence or absence of true segmentation. The apparent lack of segmentation in Echiura is considered to be either primary, thereby supporting their exclusion from Annelida, or alternatively to be the result of reduction. The latter would clearly substantiate their classification as a subtaxon of Annelida. Immunohistochemical methods and confocal laser-scanning microscopy clearly demonstrate a metameric organisation of the nervous system in different larval stages of Urechis caupo, which corresponds to the segmental arrangement of ganglia in "typical" Annelida. This segmental pattern is reflected in the serially repetitive distribution of neurons containing the neurotransmitter serotonin (5-hydroxytryptamine) and also in the corresponding distribution of strictly paired peripheral nerves. Precisely two pairs of peripheral nerves are associated with each of the repetitive units. This metameric pattern also corresponds to the transient annulation of the trunk, which is found in late larval stages. Other characters of the nervous system including the paired origin of the ventral nerve cord, the anterior-posterior development gradient and the presence of a distinct suboesophageal ganglion are also found accordingly in typical Annelida. These results are interpreted as an indication that Echiura are derived from formerly segmented ancestors, and thus support their systematic inclusion within Annelida.     

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

The nucleotide sequences of 5S rRNAs from a rotifer, Brachionus plicatilis, and two nematodes, Rhabditis tokai and Caenorhabditis elegans have been determined. The rotifer has two 5S rRNA species that are composed of 120 and 121 nucleotides, respectively. The sequences of these two 5S rRNAs are the same except that the latter has an additional base at its 3'-terminus. The 5S rRNAs from the two nematode species are both 119 nucleotides long. The sequence similarity percents are 79% (Brachionus/Rhabditis), 80% (Brachionus/Caenorhabditis), and 95% (Rhabditis/Caenorhabditis) among these three species. Brachionus revealed the highest similarity to Lingula (89%), but not to the nematodes (79%).     

Phylogeny of protostome worms derived from 18S rRNA sequences

The phylogenetic relationships of protostome worms were studied by comparing new complete 18S rRNA sequences of Vestimentifera, Pogonophora, Sipuncula, Echiura, Nemertea, and Annelida with existing 18S rRNA sequences of Mollusca, Arthropoda, Chordata, and Platyhelminthes. Phylogenetic trees were inferred via neighbor-joining and maximum parsimony analyses. These suggest that (1) Sipuncula and Echiura are not sister groups; (2) Nemertea are protostomes; (3) Vestimentifera and Pogonophora are protostomes that have a common ancestor with Echiura; and (4) Vestimentifera and Pogonophora are a monophyletic clade.      

Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: implications for lophotrochozoan phylogeny

The complete nucleotide sequences of the mitochondrial (mt) genomes of the entoprocts Loxocorone allax and Loxosomella aloxiata were determined. Both species carry the typical gene set of metazoan mt genomes and have similar organizations of their mt genes. However, they show differences in the positions of two tRNA(Leu) genes. Additionally, the tRNA(Val) gene, and half of the long non-coding region, is duplicated and inverted in the Loxos. aloxiata mt genome. The initiation codon of the Loxos. aloxiata cytochrome oxidase subunit I gene is expected to be ACG rather than AUG. The mt gene organizations in these two entoproct species most closely resemble those of mollusks such as Katharina tunicata and Octopus vulgaris, which have the most evolutionarily conserved mt gene organization reported to date in mollusks. Analyses of the mt gene organization in the lophotrochozoan phyla (Annelida, Brachiopoda, Echiura, Entoprocta, Mollusca, Nemertea, and Phoronida) suggested a close phylogenetic relationship between Brachiopoda, Annelida, and Echiura. However, Phoronida was excluded from this grouping. Molecular phylogenetic analyses based on the sequences of mt protein-coding genes suggested a possible close relationship between Entoprocta and Phoronida, and a close relationship among Brachiopoda, Annelida, and Echiura.     

The nucleotide sequences of 5S rRNAs from three ciliated protozoa.

The nucleotide sequences of 5S rRNAs from three ciliated protozoa, Paramecium tetraurelia, Tetrahymena thermophila and Blepharisma japonicum have been determined. All of them are 120 nucleotides long and the sequence of probable tRNA binding site of position 41-44 is GAAC which is characteristic of the plant 5S rRNAs. The sequence similarity percents are 87% (Paramecium/Tetrahymena), 86% (Paramecium/Blepharisma) and 79% (Tetrahymena/Blepharisma), suggesting a close relationship of these three ciliates.     

Novel aspects of the nervous system of Bonellia viridis (Echiura) revealed by the combination of immunohistochemistry, confocal laser-scanning microscopy and three-dimensional reconstruction

The Echiura have been placed in close phylogenetic affinity to the Annelida on the basis of numerous homologous characters including the mode of development, the nearly identical formation of a trochophore larva, as well as the development and ultrastructure of chaetae and spermatozoa. Furthermore, phylogenetic analysis of elongation factor-1 gene sequences supports placement of the Echiura within the Annelida. Nevertheless, the Echiura are generally excluded from the Annelida due to their lack of segmentation. However, it must be considered that this lack could represent a secondary condition and that Echiura are derived from formerly segmented ancestors. In the present study, the combination of methods applied reveals several novel aspects of the central nervous system in developmental stages of Bonellia viridis. The most important of these is the metameric organization of the ventral nerve cord. Antibodies against different neurotransmitters label discrete repetitive units of perikarya in the ventral nerve cord. This organisation is additionally supported by the distribution of peripheral nerves as shown by labelling of neurotubules. These nerves are clearly paired and are evenly distributed, corresponding to the serial units of serotoninergic neurons. Different methods of computer-aided three-dimensional reconstruction display the precise spatial distribution of perikarya and peripheral nerves allowing the repetitive units to be discerned on the basis of relative size, position and number of labelled cells. The repetitive units in the nervous system of B. viridis correspond to segmental ganglia of various Annelida and are interpreted as an indication that Echiura are derived from formerly segmented ancestors, thus supporting the systematic inclusion of the Echiura within the Annelida.     

Nucleotide sequences of chloroplast 5S ribosomal RNA from cell suspension cultures of the liverworts Marchantia polymorpha and Jungermannia subulata

The nucleotide sequences of chloroplast 5S rRNAs from cell suspension cultures of the liverworts Marchantia polymorpha and Jungermannia subulata were determined. Their nucleotide sequences, 119 nucleotides long, were highly homologous to each other (96% identity) and had high homology with those from chloroplast 5S rRNAs of two higher plants, tobacco (92% identity) and spinach (92-91% identity), but less homology (87-85% identity) with that from a lower plant, the fern Dryopteris acuminata.     

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).     

A multigene framework for polychaete phylogenetic studies

Producing a robust phylogenetic reconstruction for Polychaeta using either morphological or molecular data sets has proven very difficult. There remain many conflicts between morphological analyses and hypotheses based on DNA data, the latter principally derived from 18S rRNA sequences. For the present study a data set covering a broad range of polychaete diversity was assembled, including 38 new sequences from 21 species. Besides available 18S rRNA data, five additional gene segments were examined: the D1 and D9-10 expansion regions of 28S rRNA, histone H3, snU2 RNA and cytochrome c oxidase subunit I. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted.Annelida and Mollusca were reciprocally monophyletic in maximum likelihood analyses, but Polychaeta included a cephalopod in maximum parsimony analyses, and a patellogastropod in Bayesian analyses. When rooted on the Mollusca, optimal topologies from maximum likelihood analyses showed a recognisable basal group of taxa, including Oweniidae, Chaetopteridae and Amphinomidae. The six studied phyllodocidan families plus Orbiniidae (as the sister group of the scale-worms) formed the next most basal group. All analyses support the inclusion of Echiura, Clitellata and Siboglinidae within polychaetes. Bayesian analyses show Echiura as the sister group of Capitellidae, in agreement with previous 18S rRNA results, In contrast, Echiura formed the sister group to Trichobranchidae in maximum likelihood and maximum parsimony analyses.Supra-familial groupings consistently recovered within Polychaeta in the analyses are: (i) Terebellida without Ampharetidae; (ii) Scolecida (excepting Orbiniidae); (iii) Eunicidae, Lumbrineridae and Clitellata; and (iv) “Cirratuliformia” (including Sternaspidae) plus Sabellidae, Serpulidae and Spionidae.     

植物叶绿体4.5S核糖体rRNA作为分子杂交探针的研究

我们提取纯化了芹菜,菠菜和蕃茄叶绿体核糖体4.5SRNA(4.5SrRNA)并在其5’端标记~(32)P,作为探针与菠菜,蕃茄和芹菜叶绿体DNA(ctDNA)进行分子杂交。结果不仅证明4.5SrRNA可作为公用分子杂交探针,而且也说明不同植物4.5SrRNA序列有相当大的同源性。     

Phylogeny of protostome moulting animals (Ecdysozoa) inferred from 18 and 28S rRNA gene sequences

Reliability of reconstruction of phylogenetic relationships within a group of protostome moulting animals was evaluated by means of comparison of 18 and 28S rRNA gene sequences sets both taken separately and combined. Reliability of reconstructions was evaluated by values of the bootstrap support of major phylogenetic tree nodes and by degree of congruence of phylogenetic trees inferred by various methods. By both criteria, phylogenetic trees reconstructed from the combined 18 and 28S rRNA gene sequences were better than those inferred from 18 and 28S sequences taken separately. Results obtained are consistent with phylogenetic hypothesis separating protostome animals into two major clades, moulting Ecdysozoa (Priapulida + Kinorhyncha, Nematoda + Nematomorpha, Onychophora + Tardigrada, Myriapoda + Chelicerata, Crustacea + Hexapoda) and unmoulting Lophotrochozoa (Plathelminthes, Nemertini, Annelida, Mollusca, Echiura, Sipuncula). Clade Cephalorhyncha does not include nematomorphs (Nematomorpha). Conclusion was taken that it is necessary to use combined 18 and 28S data in phylogenetic studies.     

A contribution to sedentary polychaete phylogeny using 18S rRNA sequence data

The phylogenetic position of Annelida as well as its ingroup relationships are a matter of ongoing debate. A molecular phylogenetic study of sedentary polychaete relationships was conducted based on 70 sequences of 18S rRNA, including unpublished sequences of 18 polychaete species. The data set was analysed with maximum parsimony and maximum likelihood methods. Clade robustness was estimated by parsimony-bootstrapping and jackknifing, decay index, and clade support, as well as a posteriori probability tests using Bayesian inference. Irrespective of the applied method, some traditional sedentary polychaete taxa, such as Cirratulidae, Opheliidae, Orbiniidae, Siboglinidae and Spionidae, were recovered by our phylogenetic reconstruction. A close relationship between Orbiniidae and Questa received a particularly strong support. Echiura appears to be a polychaete ingroup taxon which is closely related to Dasybranchus (Capitellidae). As in previous molecular analyses, no support was found for the monophyly of Annelida nor for that of Polychaeta. However, we suggest that an increase in taxon sampling may yield additional resolution in the reconstruction of polychaete ingroup phylogeny, although the difficulties in reconstructing the basal phylogenetic relationships within Annelida may be due to their rapid radiation.     

The nucleotide sequences of 5S rRNAs from two red algae, Gracilaria compressa and Porphyra tenera

The nucleotide sequences of 5S rRNA from two red algae, Gracilaria compressa and Porphyra tenera have been determined. The two 5S rRNAs are fairly dissimilar to each other in their sequences (65% identity), although they are both composed of 121 nucleotides. Their secondary structures are generally of the eukaryotic with a prokaryotic characteristic. Judged from the 5S rRNA sequence data, the red algae are phylogenically distinct from green and brown algae, and they, Porphyra in particular, are evolutionally most ancient among the eukaryotes of which 5S rRNA sequence has been determined.     

Phylogeny of Molting Protostomes (Ecdysozoa) as Inferred from 18S and 28S rRNA Gene Sequences

Phylogenetic relationships within the group of molting protostomes were reconstructed by comparing the sets of 18S and 28S rRNA gene sequences considered either separately or in combination. The reliability of reconstructions was estimated from the bootstrap indices for major phylogenetic tree nodes and from the degree of congruence of phylogenetic trees obtained by different methods. By either criterion, the phylogenetic trees reconstructed on the basis of both 18 and 28S rRNA gene sequences were better than those based on the 18S or 28S sequences alone. The results of reconstruction are consistent with the phylogenetic hypothesis classifying protostomes into two major clades: molting Ecdysozoa (Priapulida + Kinorhyncha, Nematoda + Nematomorpha, Onychophora + Tardigrada, Myriapoda + Chelicerata, and Crustacea + Hexapoda) and nonmolting Lophotrochozoa (Plathelminthes, Nemertini, Annelida, Mollusca, Echiura, and Sipuncula). Nematomorphs (Nematomorpha) do not belong to the clade Cephalorhyncha (Priapulida + Kinorhyncha). It is concluded that combined data on the 18S and 28S rRNA gene sequences provide a more reliable basis for phylogenetic inferences.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 4, 2005, pp. 590–601.Original Russian Text Copyright © 2005 by Petrov, Vladychenskaya.     

Annelid phylogeny and the status of Sipuncula and Echiura

Background  

Annelida comprises an ancient and ecologically important animal phylum with over 16,500 described species and members are the dominant macrofauna of the deep sea. Traditionally, two major groups are distinguished: Clitellata (including earthworms, leeches) and "Polychaeta" (mostly marine worms). Recent analyses of molecular data suggest that Annelida may include other taxa once considered separate phyla (i.e., Echiura, and Sipuncula) and that Clitellata are derived annelids, thus rendering "Polychaeta" paraphyletic; however, this contradicts classification schemes of annelids developed from recent analyses of morphological characters. Given that deep-level evolutionary relationships of Annelida are poorly understood, we have analyzed comprehensive datasets based on nuclear and mitochondrial genes, and have applied rigorous testing of alternative hypotheses so that we can move towards the robust reconstruction of annelid history needed to interpret animal body plan evolution.     

New records of Echiura and Sipuncula in the North Atlantic Ocean, with the description of a new species of Jacobia

Data on Echiura and Sipuncula collected by the MAR-ECO expedition on the RV G.O. Sars to the northern Mid-Atlantic Ridge are presented. Eight specimens of echiuran and 13 specimens of sipunculan worms were obtained from eight stations. Two species of Echiura and two species of Sipuncula were identified. One echiuran is a new species of Jacobia.