Morphology,Morphogenesis, and Phylogeny of Urosoma caudata (Ehrenberg, 1833) Berger, 1999 (Ciliophora,Hypotrichia) based on a Chinese Population

We report the morphology and morphogenesis of Urosoma caudata (Ehrenberg, 1833) Berger, 1999 based on in vivo observation and protargol impregnation and provide an improved diagnosis of U. caudata based on previous and current work. Urosoma caudata differs from its congeners mainly by the combination of the following features: tail‐like posterior end, colorless cortical granules, and two macronuclear nodules. Urosoma caudata shares most of the ontogenetic features with its congeners: the oral primordium of the opisthe develops apokinetally, and the frontal‐ventral‐transverse cirral anlagen develop in five streaks. However, a unique morphogenetic characteristic is recognizable: the anlagen of three dorsal kineties occur de novo to the left of the parental structures differing from their intrakinetal origin in other Urosoma species. The first record of the 18S rRNA gene sequence for the species is also provided. Phylogenetic analyses based on 18S rRNA gene sequence data suggest that the genus Urosoma is a nonmonophyletic group.     

5S and 5.8S ribosomal RNA evolution in the suborder tetrahymenina (Ciliophora: Hymenostomatida)

Summary The nucleotide sequences of the 5S and 5.8S rRNAs of eight strains of tetrahymenine ciliates have been determined. The sequences indicate a clear distinction betweenTetrahymena paravorax and its suggested conspecificT. vorax, but leave the taxonomic distinction betweenT. vorax andT. leucophrys in doubt. The rRNA sequences of sixTetrahymena species and of three other species of the suborder Tetrahymenina have been used to deduce evolutionary schemes in which ancestral rRNA sequences and changes are proposed. These schemes suggest the predominant acceptance of GA and CT transitions in the 5S rDNA during the evolution of the suborder.     

Heterogeneity of intron presence/absence in Olifantiella sp. (Bacillariophyta) contributes to the understanding of intron loss

Although hypotheses have been proposed and developed to interpret the origins and functions of introns, substantial controversies remain about the mechanism of intron evolution. The availability of introns in the intermediate state is quite helpful for resolving this debate. In this study, a new strain of diatom (denominated as DB21‐1) was isolated and identified as Olifantiella sp., which possesses multiple types of 18S rDNAs (obtained from genomic DNA; lengths ranged from 2,056 bp to 2,988 bp). Based on alignments between 18S rDNAs and 18S rRNA (obtained from cDNA; 1,783 bp), seven intron insertion sites (IISs) located in the 18S rDNA were identified, each of which displayed the polymorphism of intron presence/absence. Specific primers around each IIS were designed to amplify the introns and the results indicated that introns in the same IIS varied in lengths, while terminal sequences were conserved. Our study showed that the process of intron loss happens via a series of successive steps, and each step could derive corresponding introns under intermediate states. Moreover, these results indicate that the mechanism of genomic deletion that occurs at DNA level can also lead to exact intron loss.     

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.     

Kiwifruits (Actinidia deliciosa) transformed with a Vitis stilbene synthase gene produce piceid (resveratrol-glucoside)

A stilbene synthase gene was isolated from three Vitis spp. (V. vinifera, V. labrusca and V. riparia). These genes were placed under the control of the cauliflower mosaic virus 35S promoter and introduced into kiwifruit (Actinidia deliciosa) plants by Agrobacterium-mediated gene transfer. The introduced gene(s) were expressed and piceid (resveratrol-glucoside) rather than resveratrol was produced in the leaves of the transformants. Resveratrol produced by the action of the integrated gene(s) seems to be metabolized into piceid by an endogenous glycosyltransferase. Among the transformants obtained, the highest piceid content in the young leaves was 182 μg/g fresh weight. Although these transformants did not show resistance against Botrytis cinerea, which causes gray-mould disease, the fruits may have some beneficial effects on human health. Received: 2 September 1999 / Revision received: 10 December 1999 / Accepted: 19 December 1999     

The Su(Hw) chromatin insulator protein alters double-strand break repair frequencies in the Drosophila germ line

P element-induced double-strand breaks (DSBs) on the X chromosome of Drosophila melanogaster were repaired up to four times more frequently when functional Su(Hw) chromatin insulator protein was removed from all genomic binding sites. Simultaneous comparisons of interallelic gap repair frequencies at two target loci on the X chromosome confirmed that a Su(Hw) binding site nested within a template had no effect on DSB repair efficiency. The results suggest that the genome-wide homology search of broken ends for homologous template sequences is affected because it is the only step in the recombinational repair process with an apparent genome-wide interaction. We propose that the searching 3′-hydroxy ends gain a higher degree of freedom for the search in a su(Hw) mutant background. Received: 22 September 1999; in revised form: 17 December 1999 / Accepted: 28 December 1999     

Genetic Diversity of Ostreopsis ovata (Dinophyceae) from Malaysia

The genus Ostreopsis is an important component of benthic and epiphytic dinoflagellate assemblages in coral reefs and seaweed beds of Malaysia. Members of the species may produce toxins that contribute to ciguatera fish poisoning. In this study, two species have been isolated and cultured, Ostreopsis ovata and Ostreopsis lenticularis. Analyses of the 5.8S subunit and internal transcribed spacer regions ITS1 and ITS2 of the ribosomal RNA gene sequences of these two species showed that they are separate species, consistent with morphological designations. The nucleotide sequences of the 5.8S subunit and ITS1 and ITS2 regions of the rRNA gene were also used to evaluate the interpopulation and intrapopulation genetic diversity of O. ovata found in Malaysian waters. Results showed a low level of sequence divergence within populations. At the interpopulation level, the rRNA gene sequence distinguished two groups of genetically distinct strains, representative of a Malacca Straits group (isolates from Port Dickson) and a South China Sea group (isolates from Pulau Redang and Kota Kinabalu). Part of the sequences in the ITS regions may be useful in the design of oligonucleotide probes specific for each group. Results from this study show that the ITS regions can be used as genetic markers for taxonomic, biogeographic, and fine-scale population studies of this species. Received September 15, 2000; accepted December 15, 2000     

Molecular Phylogeny of an Indian Population of Kleinstyla dorsicirrata (Foissner, 1982) Foissner et al., 2002. comb. nov. (Hypotrichia,Oxytrichidae): an Oxytrichid with Incomplete Dorsal Kinety Fragmentation

Kleinstyla dorsicirrata (Foissner, 1982) Foissner et al., 2002. comb. nov. (basionym: Gastrostyla dorsicirrata) is a slightly flexible oxytrichid, measuring about 88–115 × 27–46 μm in life and possesses cortical granules. Kleinstyla dorsicirrata is the only oxytrichid known so far with incompletely fragmented dorsal kinety. Morphological and morphogenetic data recognise K. dorsicirrata as nonstylonychine oxytrichid. Molecular phylogeny of an Indian population was inferred using 18S rRNA gene sequences and was examined with respect to oxytrichids exhibiting variation in dorsal kinety fragmentation. Kleinstyla dorsicirrata clusters with Oxytricha lanceolata; this proximity is quite significant as both show deviation from typical oxytrichid fragmentation of dorsal kinety. Molecular phylogeny of Indian population confirms its nonstylonychine oxytrichid status.     

Novel 16S rRNA gene sequences retrieved from highly saline brine sediments of Kebrit Deep, Red Sea

In this study, we report on first 16S rRNA gene sequences from highly saline brine sediments taken at a depth of 1,515 m in the Kebrit Deep, northern Red Sea. Microbial DNA extracted directly from the sediments was subjected to PCR amplification with primers specific for bacterial and archaeal 16S rRNA gene sequences. The PCR products were cloned, and a total of 11 (6 bacterial and 5 archaeal) clone types were determined by restriction endonuclease digestion. Phylogenetic analysis revealed that most of the cloned sequences were unique, showing no close association with sequences of cultivated organisms or sequences derived from environmental samples. The bacterial clone sequences form a novel phylogenetic lineage (KB1 group) that branches between the Aquificales and the Thermotogales. The archaeal clone sequences group within the Euryarchaeota. Some of the sequences cluster with the group II and group III uncultivated archaea sequence clones, while two clone groups form separate branches. Our results suggest that hitherto unknown archaea and bacteria may thrive in highly saline brines of the Red Sea under extreme environmental conditions. Received: 5 February 1999 / Accepted: 14 July 1999     

Morphological and molecular characterization of the name-bearing type species Rimaleptus binucleatus (Kahl, 1931), with a phylogenetic re-analysis of dileptid evolutionary history (Ciliophora: Litostomatea: Rhynchostomatia)

We collected Rimaleptus binucleatus from soil in the surroundings of the town of Ulsan, South Korea. Its morphology and 18S rRNA gene were studied using standard methods. This possibly widely distributed species is characterized by: (i) a size of about 170–400 × 20–65 μm; (ii) a narrowly to cylindrically dileptid body with proboscis occupying about 30–65% of body length; (iii) two dorsal contractile vacuoles; (iv) two size groups of rod-shaped extrusomes; and (v) about 18–29 ciliary rows, 4–6 of them anteriorly differentiated into a staggered dorsal brush. Phylogenetic analyses of five new rhynchostomatian 18S rRNA gene sequences supported monophylies of the orders Tracheliida and Dileptida, but revealed that the genera Rimaleptus and Pseudomonilicaryon are polyphyletic. Monophyly of genera with two macronuclear nodules was consistently rejected, but monophylies of dileptids with many scattered macronuclear nodules and of dileptids with moniliform macronucleus and multi-rowed dorsal brush could not be excluded by statistical topology tests. Nevertheless, phylogenetic network analyses indicated considerable conflict in the phylogenetic signal provided by the 18S rRNA gene to resolve unambiguously relationships among dileptid genera.     

Adding mitochondrial sequence data (16S rRNA and cytochrome c oxidase subunit I) to the phylogeny of centipedes (Myriapoda: Chilopoda): an analysis of morphology and four molecular loci

Relationships within Chilopoda (centipedes) are assessed based on 222 morphological characters, complete 18S rRNA sequences for 70 chilopod terminals, the D3 region of 28S rRNA for 65 terminals, 16S rRNA sequences for 54 terminals and cytochrome c oxidase subunit I sequences for 45 terminals. Morphological and molecular data for seven orders of Diplopoda are used to root cladograms for Chilopoda. Analyses use direct character optimization for 15 gap and substitution models. The Pleurostigmophora and Epimorpha s.l. hypotheses are largely stable to parameter variation for the combined data; the latter clade is formalized as the new taxon Phylactometria. The combined data include parameter sets that support either the monophyly of Epimorpha s.str. (=Scolopendromorpha + Geophilomorpha) or Craterostigmus + Geophilomorpha; the former derives its support from morphology and the nuclear ribosomal genes. Monophyly of Lithobiomorpha and the sister group relationship between Lithobiidae and Henicopidae are stable for morphological and combined data, and are also resolved for the molecular data for 14 of 15 parameter sets. The fundamental split in Scolopendromorpha is between Cryptopidae and Scolopendridae sensu Attems. Blind scolopendromorphs unite as a clade in most molecular and combined analyses, including those that minimize incongruence between data partitions. Geophilomorpha divides into Placodesmata and Adesmata under nine of 15 explored parameter sets.     

Morphological and molecular analysis of Aggregata aspera n. sp. (Apicomplexa: Aggregatidae) in Amphioctopus ovulum and Amphioctopus marginatus (Mollusca: Cephalopoda) from the Western Pacific Ocean

Aggregata Frenzel, 1885 (Apicomplexa) are dangerous protozoan parasites that cause malabsorption syndrome in wild and reared cephalopod species, resulting in significant economic loss to fishery and aquaculture industries. The new parasitic species, Aggregata aspera n. sp., in the digestive tract of Amphioctopus ovulum and Amphioctopus marginatus from an area in the Western Pacific Ocean was identified, it is the second two-host parasite species of Aggregata. Mature oocysts and sporocysts were spherical to ovoid in shape. Sporulated oocysts were 380.6–1,158.4 μm in length and 284.0–1,090.6 μm in width. The mature sporocysts were 16.2–18.3 μm in length and 15.7–17.6 μm in width, with irregular protuberances on the lateral wall of the sporocysts. Sporozoites within mature sporocysts were curled in shape and measured 13.0–17.0 μm in length and 1.6–2.4 μm in width. Each sporocyst contained 12–16 sporozoites. Phylogenetic tree analysis, based on 18S rRNA gene partial sequences, indicated that Ag. aspera forms a monophyletic cluster within the genus Aggregata and has a sister relationship with Ag. sinensis. These findings will provide the theoretical basis for the histopathology and diagnosis of coccidiosis in cephalopods.     

Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains

The new release of the All-Species Living Tree Project (LTP) represents an important step forward in the reconstruction of 16S rRNA gene phylogenies, since we not only provide an updated set of type strain sequences until December 2020, but also a series of improvements that increase the quality of the database. An improved universal alignment has been introduced that is implemented in the ARB format. In addition, all low-quality sequences present in the previous releases have been substituted by new entries with higher quality, many of them as a result of whole genome sequencing. Altogether, the improvements in the dataset and 16S rRNA sequence alignment allowed us to reconstruct robust phylogenies. The trees made available through this current LTP release feature the best topologies currently achievable. The given nomenclature and taxonomic hierarchy reflect all the changes available up to December 2020. The aim is to regularly update the validly published nomenclatural classification changes and new taxa proposals. The new release can be found at the following URL: https://imedea.uib-csic.es/mmg/ltp/.     

基于12S,16S和28S rRNA基因序列的中国小毛瓢虫属系统发育分析

【目的】小毛瓢虫属Scymnus Kugelann昆虫主要捕食蚜虫、蚧虫等害虫,是一类经济上重要的天敌昆虫。目前针对小毛瓢虫属的系统发育研究尚属空白,亚属之间的系统演化关系尚不明确,为了建立合理的分类系统,亟需对小毛瓢虫属的亲缘关系进行研究和探讨。【方法】以华南农业大学馆藏的小毛瓢虫属5亚属共44种为研究对象,采用PCR技术对12S, 16S和28S rRNA基因的部分序列进行扩增;运用MEGA 7.0分析了小毛瓢虫属内12S, 16S和28S rRNA基因的碱基组成,基于K2P模型计算了小毛瓢虫属44种的种间遗传距离;采用最大似然法(maximum-likelihood, ML)和贝叶斯推断法(Bayesian-inference, BI)构建该属的系统发育树。【结果】扩增获得小毛瓢虫属44种的12S rRNA基因序列平均长度为356 bp, 16S rRNA基因序列平均长度为351 bp, 28S rRNA基因序列平均长度为315 bp;序列分析表明,12S rRNA基因的A, T, G和C平均含量分别为38.8%, 43.5%, 11.9%和5.8%, 16S rRNA基因的A, T, G和C平均含量分别为37.6%, 40.3%, 14.4%和7.7%, 28S rRNA基因的A, T, G和C平均含量分别为26.7%, 18.3%, 31.4%和23.5%;基于联合序列分析的种间遗传距离为0.004～0.276,平均遗传距离为0.115。系统发育分析结果表明,小毛瓢虫属为单系起源,而小毛瓢虫亚属Scymnus(Scymnus) Kugelann、毛瓢虫亚属Scymnus(Neopullus) Sasaji、小瓢虫亚属Scymnus(Pullus) Mulsant和拟小瓢虫亚属Scymnus(Parapullus) Yang均为并系起源。【结论】基于12S, 16S和28S rRNA基因序列的小毛瓢虫属系统发育分析显示传统的形态学分类体系与基于分子数据分析的结果部分不一致,这表明应该对该属内各亚属的鉴别特征进行全面检视,筛选并确立各亚属的形态指标,同时也表明该属内的亚属分类单元需重新厘定。     

Description of a New Freshwater Ciliate Epistylis wuhanensis n. sp. (Ciliophora,Peritrichia) from China,with a Focus on Phylogenetic Relationships within Family Epistylididae

Two populations of Epistylis wuhanensis n. sp., a new freshwater peritrich ciliate, were isolated from different freshwater ponds located in Hubei, China. Their morphological characteristics were investigated using live observation, protargol impregnation, and scanning electron microscopy (SEM). Specimens from the two populations showed identical arrangement of the infraciliature and identical small subunit ribosomal RNA (SSU rRNA) gene and ITS1‐5.8S‐ITS2 sequences. The zooids present bell‐shaped and 90–175 × 27–54 μm in vivo. Macronucleus is variable in shape and located in the middle of cell. Pellicle is usually smooth with 139–154 and 97–105 striations above and below the trochal band, respectively. SSU rRNA gene and ITS1‐5.8S‐ITS2 sequences of E. wuhanensis n. sp. did not match any available sequences in GenBank. Phylogenetically, E. wuhanensis n. sp. clusters with the other Epistylis within the family Epistylididae, but is distinct from the major clades of Epistylis. Above all, the morphological characteristics and molecular analyses support that the present Epistylis is a new species. Expanded phylogenetic analyses of sessilids based on both SSU rRNA gene sequences and ITS1‐5.8S‐ITS2 sequences reveal that the genus Epistylis consists of Epistylis morphospecies and taxonomic revision of the genus is needed.     

基于线粒体16S rRNA基因对中国狼蛛科(Lycosidae)系统发育研究

将自测的中国狼蛛科Lycosidae4亚科6属26种和从GenBank中检索到的北美2种豹蛛的mtD-NA-16S rRNA序列进行比较;以漏斗蛛科1种蜘蛛作为外群,对碱基序列的组成和遗传距离进行了分析,采用Bayesian方法和最大简约法(MP)构建分子系统树。研究结果表明:16SrRNA基因的部分序列为340bp到360bp,A T含量平均为75%,存在较强的A T含量偏向性;序列共有157个碱基存在变异,其中79个简约信息位点。狼蛛科各属间的遗传距离介于0.026￣0.200之间。2种建树方法均表明:科内的属及属内的种优先聚在一起;水狼蛛属相对马蛛属是狼蛛科中较为原始的类群,分化较早;獾蛛属作为1个单系群与熊蛛属合为1个并系,属于狼蛛亚科。狼蛛科6属间的分子系统关系为(Pirata(Hippasa(Trochsa Arctosa(Pardosa Wadicosa))))。     

Morphology and Phylogenetic Position of an Unusual Stentor polymorphus (Ciliophora: Heterotrichea) Without Symbiotic Algae

We investigated the live morphology, infraciliature, and small subunit rRNA gene sequences of an unusual population of Stentor polymorphus without symbiotic algae that was isolated from the southeastern region of Brazil. The morphological and molecular data confirmed the identity of this strain as S. polymorphus. The Brazilian S. polymorphus organism is 850–2,000 μm in length in vivo and has colorless cortical granules, a moniliform macronucleus with 6–12 nodules, somatic ciliature composed of 50–60 kineties, a single contractile vacuole located to the left of the cytostome, and a conspicuous oral pouch, and it does not build a lorica. Based on the phylogenetic analyses, the Brazilian S. polymorphus was located within a cluster consisting of four other S. polymorphus sequences, with high support values using both the Bayesian inference and maximum likelihood algorithms. Our study presents the first report of a S. polymorphus population without its symbionts under natural conditions. On the basis of our findings, we propose that the presence or absence of symbiotic algae should not be used as a taxonomic character for the identification of Stentor species.     

Molecular Analysis of Ribosomal RNA Gene of Red Tide Algae Obtained from the Seto Inland Sea

Eleven clones from five species of the planktonic microalgae, (Chattonella antiqua, Chattonella marina, Heterosigma akashiwo, Alexandrium catenella, and Scrippsiella trochoidea), which were collected from the Seto Inland Sea in Japan and from Thailand, were subjected to nucleotide sequence analysis of the D1/D2 domain of the large subunit (LSU) of their ribosomal RNA genes. After amplification by polymerase chain reaction using degenerated primers, whole-nucleotide sequences for the D1/D2 domains of the LSU rRNA gene of 11 microalgae were analyzed. Phylogenic tree analysis using these nucleotide sequences showed each species located in a cluster corresponding to its morphological classification. The nucleotide sequence data for Chattonella spp. suggest that multiple clones of both Chattonella antiqua and Chattonella marina are present in the Seto Inland Sea and that red tide blooms of Chattonella spp. in different years may have contained different clones. Received September 6, 1999; accepted December 16, 1999.