Achlya abortispora, a New Oomycete Isolated from Water Samples Taken from a Water Reservoir in Morocco

Achlya abortispora sp. nov. was found in water and floating organic matter taken form a dam near Rabat, Morocco. The new species is described and compared with other species of the genus. Distinguishing characteristics of A. abortispora are the production of long fusiform sporangia with achlyoid and aplanoid discharge of zoospores; smooth-walled spherical to club-shaped oogonia, which are usually lateral, but at times intercalary, containing 1 to 20 oospheres. The oogonia can also bear 1 to 5 appendages, which may indicate oogonial proliferation. Most of the oospheres do not mature and are thus abortive. The antheridial branches supplying the oogonia are predominantly diclinous, but at times these may be monoclinous and androgynous. Antheridial branches coil and wrap around the oogonia. Morphologic features of the oomycete and the sequence of the ITS region of its rDNA, as well as their comparison with related species, are discussed. This is the first report of the occurrence of a saprolegniaceous oomycete from Morocco.     

Genealogical analyses of multiple loci of litostomatean ciliates (Protista, Ciliophora, Litostomatea)

The class Litostomatea is a highly diverse ciliate taxon comprising hundreds of free-living and endocommensal species. However, their traditional morphology-based classification conflicts with 18S rRNA gene phylogenies indicating (1) a deep bifurcation of the Litostomatea into Rhynchostomatia and Haptoria+Trichostomatia, and (2) body polarization and simplification of the oral apparatus as main evolutionary trends in the Litostomatea. To test whether 18S rRNA molecules provide a suitable proxy for litostomatean evolutionary history, we used eighteen new ITS1-5.8S rRNA-ITS2 region sequences from various free-living litostomatean orders. These single- and multiple-locus analyses are in agreement with previous 18S rRNA gene phylogenies, supporting that both 18S rRNA gene and ITS region sequences are effective tools for resolving phylogenetic relationships among the litostomateans. Despite insertions, deletions and mutational saturations in the ITS region, the present study shows that ITS1 and ITS2 molecules can be used to infer phylogenetic relationships not only at species level but also at higher taxonomic ranks when their secondary structure information is utilized to aid alignment.     

Pythium ornacarpum: a new species with ornamented oogonia isolated from soil in France

Pythium ornacarpum sp. nov. was isolated from a soil sample taken from Genlis in the Burgundy region of France. This species is unique because of its ornamented oogonia which are completely surrounded by antheridial filaments. The fungus is closely related to Pythium echinulatum Matthews. Morphological and reproductive aspects of this species as well as a study by PCR of the sequence of the internal transcribed spacer (ITS1) of the nuclear ribosomal gene and its comparison with related species are described here. The nucleotide sequence of the ITS1 region flaking the 5.8S rRNA of this species and other related species are also given here.     

A secondary structural common core in the ribosomal ITS2 (internal transcribed spacer) of Culexspecies from diverse geographical locations

In the present study, sequence and structural analysis of ITS2 region (the spacer segment between 5.8S and 28S rRNA of mature rRNA sequences) of 7 Culex species belonging to 5 different geographical locations was carried out. Alignment of the ITS2 sequence from the 7 species revealed 8 homologous domains. Four species namely C. vishnui, C. annulus, C. pipiens, C. quiquefasciatusshowed high sequence (98-100%) and RNA secondary structure similarity. The ITS2 similarity among different species is high despite their varying geographical locations. Several common features of secondary structure are shared among these species, with some of them supported by compensatory changes, suggesting the significant role by ITS2 as an RNA domain during ribosome biogenesis.     

Pythium carbonicum,a new species isolated from a spoil heap in northern France,the ITS region,taxonomy and comparison with related species

Pythium carbonicum (F-72) sp. nov. was found in soil samples taken on the top of a spoil heap in northern France. The morphology of this new species resembles that of a recently described species: Pythium megacarpum. However, the antheridial and oogonial characteristics of this new species are unique, and the comparison of its ITS region of the nuclear ribosomal DNA indicates that this species is also related to the genus Phytophthora. The fungus does not sporulate, the sporangia germinate directly into mycelium through germ tubes. The oogonia of P. carbonicum are smooth-walled and also papillated, and are provided with monoclinous and diclinous antheridia that wrap around, forming a complicated knot. Morphological features of this new species, together with the sequences of the ITS region of its nuclear ribosomal DNA and its comparison with related species are discussed here.     

Nucleotide sequence diversity of rDNA internal transcribed spacers extracted from conidia and cleistothecia of several powdery mildew fungi

An improved protocol, including DNA extraction with Chelex, two amplifications with a nested primer set, and DNA purification by electrophoresis, made it possible to analyze nuclear rDNA sequences of powdery mildew fungi using at most several hundred conidia or 20 cleistothecia. Nucleotide sequence diversity of the nuclear rDNA region containing the two internal transcribed spacers (ITS1 and ITS2) and 5.8S rRNA gene derived from conidia and cleistothecia was investigated for four kinds of powdery mildew fungi including two isolates of the same species. The results showed that the nucleotide sequences of the nuclear rDNA region were highly conserved between the teleomorph and the anamorph. Thus, the nucleotide sequence data obtained from either developmental stage can be used for phylogenetic studies of powdery mildew fungi. The nucleotide sequences of the 5.8S rRNA genes of the four species were highly conserved, but those of their ITS regions were variable. This suggests that the nuclear rDNA region is not suitable for phylogenetic studies of distantly related powdery mildew fungi, because too much sequence diversity exists, within the ITS, and too little phylogenetic information is contained within the 5.8S rRNA gene. However, the ITS region will be useful for phylogenetic comparison of closely related species or intraspecies. Contribution No. 132 from the Laboratory of Plant Pathology, Mie University.     

Molecular characterization of Histomonas meleagridis and other parabasalids in the United States using the 5.8S, ITS-1, and ITS-2 rRNA regions

Extracted DNA from 28 Histomonas meleagridis -infected avian tissue samples from multiple hosts and geographic locations was analyzed for variation in the 5.8S rRNA and the flanking internal transcribed spacer regions (ITS 1 and ITS 2). Samples were amplified by polymerase chain reaction, sequenced, and compared with known sequences from GenBank accessions of H. meleagridis and other related protozoa. The analyses revealed significant genetic variation within H. meleagridis sequences and suggested the possibility of multiple genotypes within the samples or a possible misdiagnosis. Related protozoa found in some samples were mostly identified as Tetratrichomonas spp. However, 1 sample had a 93% identity to Simplicimonas similis , a newly described organism, suggesting the possibility of a new pathogen in poultry. A phylogenetic tree analyzing the 5.8S and flanking ITS regions was inconclusive and we were unable to resolve all H. meleagridis into a single grouping. In contrast, a tree constructed only on the 5.8S rRNA grouped all but 1 H. meleagridis sample into 1 clade, including GenBank accessions submitted from Europe. This suggests that the 5.8S region alone is more reliable in identifying H. meleagridis than are the combined 5.8S and flanking ITS regions. There was no correlation between genotypes and host species or geographic location, suggesting that H. meleagridis moves freely between multiple avian species in the sampled regions.     

Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae).

The internal transcribed spacer (ITS) region of the ribosomal DNA from the European scallops Aequipecten opercularis, Mimachlamys varia, Hinnites distortus, and Pecten maximus was PCR amplified and sequenced. For each species, three or five clones were examined. The size ranged between 636 and 713 bp (ITS1, 209-276 bp; 5.8S rRNA gene, 157 bp; ITS2, 270-294 bp) and GC content ranged between 47 and 50% (ITS1, 43-49%; 5.8S rRNA gene, 56-57%; ITS2, 44-49%). Variation within repeats was minimal; only clones from M. varia and P. maximus displayed a few variable sites in ITS2. Among scallops, including Chlamys farreri whose ITS sequence appears in databases, significant variation was observed in both ITS1 and ITS2. Phylogenetic analysis using ITS1, ITS2, or both spacer sequences always yielded trees with similar topology. Aequipecten opercularis and P. maximus grouped in one clade and the other three scallops (C. farreri, M. varia, and H. distortus) in another, where M. varia and H. distortus are the more closely related species. These results provide new insights into the evolutionary relationships of scallop species and corroborate the close evolutionary relationship between the tribes Aequipectinini and Pectinini previously deduced from 18S rDNA sequences.     

The final step in the formation of 25S rRNA in Saccharomyces cerevisiae is performed by 5'-->3' exonucleases

The final stage in the formation of the two large subunit rRNA species in Saccharomyces cerevisiae is the removal of internal transcribed spacer 2 (ITS2) from the 27SB precursors. This removal is initiated by endonucleolytic cleavage approximately midway in ITS2. The resulting 7S pre-rRNA, which is easily detectable, is then converted into 5.8S rRNA by the concerted action of a number of 3'-->5' exonucleases, many of which are part of the exosome. So far the complementary precursor to 25S rRNA resulting from the initial cleavage in ITS2 has not been detected and the manner of its conversion into the mature species is unknown. Using various yeast strains that carry different combinations of wild-type and mutant alleles of the major 5'-->3' exonucleases Rat1p and Xrn1p, we now demonstrate the existence of a short-lived 25.5S pre-rRNA whose 5' end is located closely downstream of the previously mapped 3' end of 7S pre-rRNA. The 25.5S pre-rRNA is converted into mature 25S rRNA by rapid exonucleolytic trimming, predominantly carried out by Rat1p. In the absence of Rat1p, however, the removal of the ITS2 sequences from 25.5S pre-rRNA can also be performed by Xrn1p, albeit somewhat less efficiently.     

cpcHID操纵子序列用于钝顶节旋藻品系分类与鉴定的研究

克隆并测定7株钝顶节旋藻品系的cpcHID操纵子序列,以及16SrRNA和16S-23SrRNA转录单元内间隔区(ITS)序列,进一步通过生物信息学和分子系统学等研究发现:(1)7株品系的cpcHID序列,以及16SrRNA和ITS序列具有很高的相似性。(2)基于7株品系cpcHID序列的GC含量绝对偏差平均值、碱基变异率和遗传距离系数普遍比基于16SrRNA和ITS序列的大。(3)基于cpcHID序列的分类结果与基于16SrRNA和ITS序列的十分相近。因此,cpcHID可作为节旋藻等蓝细菌分类与鉴定的一种新的分子标记,特别是以其丰富的信息量而在品系水平的分类鉴定中占有优势。     

A new microsporidian parasite, Heterosporis saurida n. sp. (Microsporidia) infecting the lizardfish, Saurida undosquamis from the Arabian Gulf, Saudi Arabia: ultrastructure and phylogeny

A new microsporidian that infects the lizardfish Saurida undosquamis (Richardson, 1848) that are caught in the Arabian Gulf in Saudi Arabia is described here. This parasite invades the skeletal muscle of the abdominal cavity forming white, cyst-like structures containing numerous spores. The prevalence of the infection was 32·1% (135/420). The spores were oval to pyriform in shape and measured approximately 3·3 μm×2·0 μm. The developing spores were found within parasitophorous vacuoles. In mature spores, the polar filament was arranged into 5 coils in a row. Molecular analysis of the rRNA genes, including the ITS region, and phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference were performed. The ultrastructural characteristics and phylogenetic analyses support the recognition of a new species, herein named Heterosporis saurida n. sp.