The nucleotide sequence ofBeneckea harveyi 5S rRNA

Summary The complete sequence of the 5S rRNA from the bioluminescent bacterium,Beneckea harveyi has been determined to be p U G C U U G G C G C C A U A G C G A U U-G G A C C C A C U G A (U) C U U C A U U C C-G A A C C A G A A G U G A A C G A A U U A-G G C C G A U G G U G U G U G G G G C U-C C C C A U G U A G A G U A G G A A U C G-C C A G G U (U)_OH.Two sites of sensitivity to ribonuclease T₂ cleavage were identified; at A₄₁ and either A₅₄ or A₅₅. Comparison with existing sequence information fromEscherichia coli andPhotobacterium phosphoreum clarifies the amount of diversity among the bioluminescent bacteria and provides further insight into their phylogenetic position. Sequence heterogeneities were encountered and the importance of these in interpreting 5S rRNA data is discussed.     

三线闭壳龟18SrRNA基因序列的测定

用分子遗传标记进行物种鉴别准确可靠,本文应用18SrRNA序列测定研究中药材三线闭壳龟的进化与种类鉴定.应用PCR直接测序技术测定三线闭壳龟肌肉18srRNA基因部分核苷酸序列.结果表明,所测序列为678bp,其中GC占多数(54.1%).讨论了DNA测序技术在龟鳖类等中药材鉴定方面的应用.     

The 16S rRNA nucleotide sequence of Mycobacterium leprae: phylogenetic position and development of DNA probes

The almost complete 16S rRNA sequence from Mycobacterium leprae was determined by direct sequencing of the chromosomal gene amplified by the polymerase chain reaction. The primary sequence revealed an insertion of 12 nucleotides at the 5' end of the 16S rRNA gene, which consists of an A-T stretch and appears to be unique for M. leprae. Within the mycobacteria M. leprae branches off with a group of slow-growing species comprising M. scrofulaceum, M. kansasii, M. szulgai, M. malmoense, M. intracellulare and M. avium. A systematic comparison of the nucleotide sequence resulted in the characterization of oligonucleotide probes which are highly specific for M. leprae. The probes hybridized exclusively to 16S rRNA nucleic acids from M. leprae, but not to nucleic acids from 20 cultivable fast- and slow-growing mycobacteria.     

Bacterial phylogeny based on 16S and 23S rRNA sequence analysis

Abstract: Molecular phylogeny increasingly supports the understanding of organismal relationships and provides the basis for the classification of microorganisms according to their natural affiliations. Comparative sequence analysis of ribosomal RNAs or the corresponding genes currently is the most widely used approach for the reconstruction of microbial phylogeny. The highly and less conserved primary and higher order structure elements of rRNAs document the history of microbial evolution and are informative for definite phylogenetic levels. An optimal alignment of the primary structures and a careful data selection are prerequisites for reliable phylogenetic conclusions. rRNA based phylogenetic trees can be reconstructed and the significance of their topologies evaluated by applying distance, maximum parsimony and maximum likelihood methods of phylogeny inference in comparison, and by fortuitous or directed resampling of the data set. Phylogenetic trees based on almost equivalent data sets of bacterial 23S and 16S rRNAs are in good agreement and their overall topologies are supported by alternative phylogenetic markers such as elongation factors and ATPase subunits. Besides their phylogenetic information content, the differently conserved primary structure regions of rRNAs provide target sites for specific hybridization probes which have been proven to be powerful tools for the identification of microbes on the basis of their phylogenetic relationships.     

鸡球虫18S rRNA基因序列的测定与分析

为了利用18S rRNA基因进行鸡球虫系统进化分析,对巨型艾美耳球虫(Eimeria maxima)、柔嫩艾美耳球虫(E.tenella)、堆形艾美耳球虫(E.acervulina)3种共8个不同来源的虫株,分别提取总DNA进行18S rRNA基因的扩增和测序;将得到的序列登录GenBank进行同源性和趋异性分析,并结合GenBank中其它原虫的18S rRNA基因序列构建进化树.结果显示扩增获得8株鸡球虫18S rRNA基因长度为1746～1756 bp,序列比对显示同种不同株间的同源性大于不同种间的同源性,其中3株E.maxima株间同源性在98.7%～99.3%之间,4株E.tenella株间同源性在99.7%～99.9%之间;不同种间同源性为96.5%～98.1%,其中E.maxima与E.tenclla的遗传距离最大,为0.038;E.maxima与E.acervulina的遗传距离最小,为0.021.顶复器门9个不同属所构建的进化树结果显示,E.imeria和等孢属(Isospora)聚为一支,说明亲缘关系比较近.与GertBank中其它5株不同鸡球虫的18S rRNA基因共同构建的进化树显示,3株E.maxima聚为一支,与E.brunetti、E.mitis、E.mivati、E.praecox和E.acervulina聚为一大分支;4株E.tenella与1株E.necatrix共同形成一个分支,说明E.tenella与E.necattix的亲缘关系最近.本研究证实了在鸡球虫系统进化研究中,18S rRNA基因不仅可以区分不同种,而且有可能成为区分同种不同株的理想靶基因.     

Comparison of the nucleotide sequence of soybean 18S rRNA with the sequences of other small-subunit rRNAs

Summary We present the sequence of the nuclearencoded ribosomal small-subunit RNA from soybean. The soybean 18S rRNA sequence of 1807 nucleotides (nt) is contained in a gene family of approximately 800 closely related members per haploid genome. This sequence is compared with the ribosomal small-subunit RNAs of maize (1805 nt), yeast (1789 nt),Xenopus (1825 nt), rat (1869 nt), andEscherichia coli (1541 nt). Significant sequence homology is observed among the eukaryotic small-subunit rRNAs examined, and some sequence homology is observed between eukaryotic and prokaryotic small-subunit rRNAs. Conserved regions are found to be interspersed among highly diverged sequences. The significance of these comparisons is evaluated using computer simulation of a random sequence model. A tentative model of the secondary structure of soybean 18S rRNA is presented and discussed in the context of the functions of the various conserved regions within the sequence. On the basis of this model, the short basepaired sequences defining the four structural and functional domains of all 18S rRNAs are seen to be well conserved. The potential roles of other conserved soybean 18S rRNA sequences in protein synthesis are discussed.     

Bacterial,archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis

We studied the microbial diversity in the sediment from the Kongsfjorden, Svalbard, Arctic, in the summer of 2005 based on the analysis of 16S rRNA and 18S rRNA gene clone libraries. The sequences of the cloned 16S rRNA and 18S rRNA gene inserts were used to determine the species identity or closest relatives by comparison with sequences of known species. Compared to the other samples acquired in Arctic and Antarctic, which are different from that of ours, the microbial diversity in our sediment is much higher. The bacterial sequences were grouped into 11 major lineages of the domain Bacteria: Proteobacteria (include α-, β-, γ-, δ-, and ε-Proteobacteria); Bacteroidetes; Fusobacteria; Firmicutes; Chloroflexi; Chlamydiae; Acidobacteria; Actinobacteria; Planctomycetes; Verrucomicrobiae and Lentisphaerae. Crenarchaeota were dominant in the archaeal clones containing inserts. In addition, six groups from eukaryotes including Cercozoa, Fungi, Telonema, Stramenopiles, Alveolata, and Metazoa were identified. Remarkably, the novel group Lentisphaerae was reported in Arctic sediment at the first time. Our study suggested that Arctic sediment as a unique habitat may contain substantial microbial diversity and novel species will be discovered.     

基于18S rRNA的中国大陆沿海石磺科贝类分类的初步分析

对采自上海崇明、福建宁德、海南海口等沿海地区9个群体的石磺科贝类进行外部形态特征差异分析和内部结构比较,在初步分类基础上利用核糖体小亚基18S rRNA基因部分序列对9个群体进行系统发育分析,以菊花螺为外群,结合GenBank上石磺科4个18S rRNA基因序列构建系统发生树来探讨我国大陆沿海石磺科属种间的亲缘关系.结果显示:我国石磺科贝类南方沿海种类多于北方沿海;除报道的瘤背石磺(Onchidium struma)和石磺(O.verruculatum)外,可能还有新记录5种:Onchidium属1种、Platevindex属2种、Peronia属1种和Paraoncidium属1种.分子系统发生树显示,我囝大陆沿海石磺科9个群体可分为4个亚群,分别为Onchidium、Platevindex、Paraoncidium、Peronia,其中Peronia亚群的置信度较高;Onchidium verruculatum应更名为Peronia verruculata.     

16S rRNA gene sequence analyses and inter- and intrageneric relationships of Xanthomonas species and Stenotrophomonas maltophilia

The nearly complete, PCR-amplified, 16S rRNA gene sequences have been determined from the representative type strains of eight xanthomonad phena, including six validly described species of the genus Xanthomonas and Stenotrophomonas maltophilia. Pairwise sequence comparisons and phylogenetic analysis demonstrated that the xanthomonads comprise a monophyletic lineage within the γ-subclass of the Proteobacteria. Although the genus Xanthomonas was observed to comprise a cluster of very closely related species, the observed species-specific primary sequence differences were confirmed through sequencing additional strains belonging to the respective species.     

The diversity of fungi in aerobic sewage granules assessed by 18S rRNA gene and ITS sequence analyses

Aerobic sewage granules are dense, spherical biofilms, regarded as a useful and promising tool in wastewater treatment processes. Recent studies revealed that fungi can be implemented in biofilm formation. This study attempts to uncover the fungal diversity in aerobic granules by sequence analysis of the 18S and 5.8S rRNA genes and the internal transcribed spacer regions. For this purpose, appropriate PCR and sequencing primer sets were selected and an improved DNA isolation protocol was used. The sequences of 41 isolates were assigned to the taxonomic groups Pleosporaceae, Xylariales, Theleobolaceae, Claviceps, Aureobasidium, Candida boleticola , and Tremellomycetes within the fungi. It turned out that the fungal community composition in granules depended on the wastewater type and the phase of granule development.     

Phylogenetic consideration of two scuticociliate genera, Philasterides and Boveria (Protozoa, Ciliophora) based on 18 S rRNA gene sequences

Many scuticociliates are facultative parasites of aquatic organisms and are among the most problematic ciliate taxa regarding their systematic relationships. The main reason is that most species, especially taxa in the order Thigmotrichida have similar morphology and have not been studied yet using molecular methods. In the present work, two scuticociliate genera, represented by two rare parasitic species, Philasterides armatalis (order Philasterida) and Boveria subcylindrica (order Thigmotrichida), were studied, and phylogenetic trees concerning these two genera were constructed based on their 18 S rRNA gene sequences. The results indicate that: 1) Philasterides forms a sister group with Philaster, supporting the classification that these two genera belong to the family Philasteridae; 2) it is confirmed that the nominal species, Philasterides dicentrarchi Dragesco et al., 1995 should be a junior synonym of Miamiensis avidus as revealed by both previous investigations and the data revealed in the present work; and 3) the poorly known form B. subcylindrica, the only member in the order Thigmotrichida, of which molecular data are available so far, always clusters with Cyclidium glaucoma, a highly specialized scuticociliate, indicating a sister relationship between the orders Thigmotrichida and Pleuronematida.     

双壳纲贝类18S rRNA基因序列变异及系统发生

双壳纲贝类栖息于环境多变的海域,是一个形态学和生态学都具有多样性的类群,清晰而可靠的进化关系对于养殖与相关种类的管理具重要意义。然而,目前对双壳类宏观分子系统学研究的报道较少。研究用18S rRNA基因(18S)分析了双壳类3个亚纲贝类的系统发育关系。从GenBank下载帘蛤目、海螂目、贻贝目、胡桃蛤目、蚶目、珍珠贝目6个目94个种类的18S全/部分序列107个,通过ClustalX软件进行序列比对, 用MEGA4.1软件和PHyML软件计算遗传距离, 构建系统发育树, 研究了双壳类18S变异规律及其在系统发生研究中的应用。结果显示18S有插入/缺失序列, 存在长度多态性。序列比对显示有5段约30 70bp的保守区, 4段约130 550bp的高变区。碱基组成平均为T:24.4%, C:23.6%, A:24.5%, G:27.5%。G+C含量为51.1%。在1796个比对位点中, 变异位点占31.7%, 简约信息位点占24.0%。目内科间遗传距离为0.003 0.043, 目间遗传距离为0.026 0.093。NJ树和ML树显示贻贝目、珍珠贝目、胡桃蛤目、蚶目和海螂目的缝栖蛤科先分别聚为支持率很高(BPN=94 100)的单系支, 后聚为一大支(BPN=100)。蛤蜊科与帘蛤目的其他科分离形成一置信度很高的单系支(BPN=93)。帘蛤科种类聚为置信度较低(BPN=60)的一支。海螂目、帘蛤目的种类没能完全聚到所属支系, 彼此嵌套,缝栖蛤科的种类从海螂目中分离出来。18S资料揭示帘蛤目的蛤蜊科、海螂目的缝栖蛤科已经进化为独立的支系。     

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.     

Phylogenetic position of an arbuscular mycorrhizal fungus,Acaulospora gerdemannii, and its synanamorphGlomus leptotichum, based upon 18S rRNA gene sequence

We examined the phylogenetic position of an arbuscular mycorrhizal fungus which produces two types of spore,Acaulospora gerdemannii andGlomus leptotichum, based upon the DNA sequence of the 18S rRNA gene. DNA was extracted separately from bothGlomus-like orAcaulospora-like spores and partial 5′-terminus segments of 18S rRNA gene were amplified by the PCR method. Several clones derived from each spore type were sequenced and compared. The sequences from both spore types agreed well, confirming that these morphologically different spores were formed by the same fungus. Nucleotide substitutions were found among several clones, suggesting polymorphism of the rRNA gene in glomalean fungi. Further phylogenetic analysis based upon the whole sequence of the 18S rRNA gene showed thatA. gerdemannii may be within the order Glomales but is far from the fungi that have been analyzed and probably should be in a new family.     

The phylogeny of Mycoplasma bovis as determined by sequence analysis of the 16S rRNA gene

Abstract The nucleotide sequence of the 16S rRNA gene of Mycoplasma bovis has been determined. Comparisons with other 16S rRNA sequences of mycoplasmas showed that Mycoplasma agalactiae is phylogenetically the closet relative. In total, only eight nucleotides differed between the M. bovis and M. agalactiae 16S rRNA sequences. The phylogenetic position of M. bovis with respect to other mycoplasmas was determined by sequence comparisons and from features in the secondary structure of 16S rRNA.     

Phylogenetic relationships of Serpulidae (Annelida: Polychaeta) based on 18S rDNA sequence data, and implications for opercular evolution

Phylogenetic relationships of (19) serpulid taxa (including Spirorbinae) were reconstructed based on 18S rRNA gene sequence data. Maximum likelihood, Bayesian inference, and maximum parsimony methods were used in phylogenetic reconstruction. Regardless of the method used, monophyly of Serpulidae is confirmed and four monophyletic, well-supported major clades are recovered: the Spirorbinae and three groups hitherto referred to as the Protula-, Serpula-, and Pomatoceros-group. Contrary to the taxonomic literature and the hypothesis of opercular evolution, the Protula-clade contains non-operculate (Protula, Salmacina) and operculate taxa both with pinnulate and non-pinnulate peduncle (Filograna vs. Vermiliopsis), and most likely is the sister group to Spirorbinae. Operculate Serpulinae and poorly or non-operculate Filograninae are paraphyletic. It is likely that lack of opercula in some serpulid genera is not a plesiomorphic character state, but reflects a special adaptation.     

Phylogenetic placement of the basidiomycetous yeastsKondoa malvinella andRhodosporidium dacryoidum,and the anamorphic yeastSympodiomycopsis paphiopedili by means of 18S rRNA gene sequence analysis

The 18S ribosomal RNA gene sequences of the basidiomycetous yeastsKondoa malvinella andRhodosporidium dacryoidum, and an anamorphic yeastSympodiomycopsis paphiopedili were determined. The 18S rRNA gene ofR. dacryodium IAM 13522 (ex type) revealed the presence of an intron-like region with a length of 404 nucleotides, which is presumably assigned to a group I intron. The phylogenetic tree, including 34 published reference sequences, was inferred from 1493 sites which could be unambiguously aligned. The molecular phylogeny, using the ascomycetes as an outgroup, divided the basidiomycetes into three major lineages. The first lineage was composed of the smut fungi (Ustilaginales), represented byUstilago maydis, U. hordei, andTilletia caries, includingS. paphiopedili. The second lineage included the type species of teliospore-forming yeast generaLeucosporidium, Rhodosporidium, andSporidiobolus, and the generaErythrobasidium andKondoa, both previously included in the Filobasidiaceae.Rhodosporidium dacryodium showed a close relationship withE. hasegawianum, which was backed by a high bootstrap support. The rust fungiCronartium ribicola andPeridermium harknessii were also included in this lineage. The last lineage was formed by the filobasidiaceous yeasts,Cystofilobasidium capitatum, Mrakia frigida, Filobasidium floriforme, andFilobasidiella neoformans, and the anamorphic yeastsBullera alba (the anamorph ofBulleromyces albus) andTrichosporon cutaneum. Members ofTremella and selected hymenomycetous genera were also included in this lineage.The nucleotide sequence data reported in this paper will appear in the GSDB, DDBJ, EMBL and NCBI nucleotide sequence databases with the following accession numbers D13459 (Rhodosporidium dacryodium), D13776 (Kondoa malvinella), and D14006 (Sympodiomycopsis paphiopedili).     

Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data

The complete sequence of the 18 S ribosomal RNA gene(18S rRNA) from Lymantria dispar was cloned and analysed here. 18 S rRNA and mitochondrial cytochrome c oxidasel(cox1) gene sequences of Lymantria dispar were compared with homologous sequences of other nine insects from different orders. Analytic results showed that 18 S rRNA of these insects had two conserved domains and the second domain was an even more conserved region. The phylogenetic trees based on the full-length sequence and the second domain fragment of 18 S rRNA as well as sequence of cox1 from different orders indicated that Lepidoptera and Trichoptera, which belongs to Amphiesmenoptera, had a closer phylogenetic relationship and fewer differences were observed comparing with traditional taxonomic results.