The pseudouridine residues of ribosomal RNA

1995 ◽  
Vol 73 (11-12) ◽  
pp. 915-924 ◽  
Author(s):  
James Ofengand ◽  
Andrei Bakin ◽  
Jan Wrzesinski ◽  
Kelvin Nurse ◽  
Byron G. Lane
Keyword(s):  
Ribosomal Rna ◽  
Large Subunit ◽  
Small Subunit ◽  
Modified Nucleosides ◽  
Peptidyl Transferase ◽  
Functional Roles ◽  
Structural Types ◽  
Representative Species ◽  
Sequencing Technique ◽  
Nucleotide Resolution

Pseudouridine (Ψ), the most common single modified nucleoside in ribosomal RNA, has been positioned in the small subunit (SSU) and large subunit (LSU) RNAs of a number of representative species. Most of the information has been obtained by application of a rapid primed reverse transcriptase sequencing technique. The locations of these Ψ residues have been compared. Many sites for Ψ are the same among species, but others are distinct. In general, the percentage Ψ in multicellular eukaryotes is greater than in prokaryotes. In LSU RNA, the Ψ residues are strongly clustered in three domains, all of which are near or connected to the peptidyl transferase center. There is no apparent clustering of Ψ in SSU RNA. The Ψ sites in LSU RNA overlap those for the methylated nucleosides, but this is not the case in SSU RNA. There are 265 Ψ sites known to nucleotide resolution, of which 246 are in defined secondary structures, and 112 of these are in nonidentical structural contexts. All 246 Ψ sites can be classified into five structural types. Two Escherichia coli Ψ synthases have been cloned and characterized, one for Ψ516 in SSU RNA and one for Ψ746 in LSU RNA. The Ψ746 synthase recognizes free RNA, but the Ψ516 enzyme requires an intermediate RNP particle. Possible functional roles for Ψ in the ribosome are discussed.Key words: pseudouridine, sequencing, modified nucleosides, ribosomal RNA.

New observations on Miculenchus Andrássy, 1959 (Nematoda: Tylenchidae) with descriptions of two new and one known species from Iran

Nematology ◽  
2019 ◽  
Vol 21 (9) ◽  
pp. 937-956 ◽  
Author(s):  
Yousef Panahandeh ◽  
Ebrahim Pourjam ◽  
Sergio Álvarez-Ortega ◽  
Farahnaz Jahanshahi Afshar ◽  
Majid Pedram
Keyword(s):  
New Species ◽  
Ribosomal Rna ◽  
Large Subunit ◽  
Small Subunit ◽  
Lsu Rdna ◽  
Natural Forests ◽  
Electron Microscopic ◽  
Pharyngeal Bulb ◽  
Ribosomal Rna Gene ◽  
Molecular Approaches

Summary During nematological surveys in grasslands and natural forests of north and north-western Iran, three species of Miculenchus, including two new and one known species, were recovered and characterised based upon morphological and molecular approaches. Miculenchus brevisalvus n. sp., the first new species, is mainly characterised by its short females 334-388 μm long and with a short 6.0-7.5 μm long stylet, pyriform to pyriform-elongate pharyngeal bulb, 4-8 μm long post-uterine sac (PUS), offset rounded spermatheca filled with small spheroid sperm, elongate conoid tail 62-83 μm long with a sharp tip, and males with simple cloacal lips. Miculenchus muscus n. sp., the second new species, is characterised by a combination of the following features: body 401-467 μm long, well-developed protuberant labial plate at the anterior end under light microscopy, stylet 7-9 μm long, pyriform pharyngeal bulb, PUS 4-9 μm long, gradually narrowing conical tail 62-74 μm long with a finely pointed or sharp end and bearing several fine bristles at tip, and a male with projecting cloacal lips. Both newly described species were morphologically compared with four currently known species of the genus, viz., M. elegans, M. salmae, M. salvus, and M. tesselatus. Miculenchus salmae was also recovered and reported from Iran for the first time. It is mainly characterised by lacking a PUS and the characteristic vagina shape. Miculenchus muscus n. sp. and M. salmae were both characterised using scanning electron microscopic images, yielding new morphological observations for the genus. All three species are studied for their molecular phylogenetic characters using sequences of near-full length fragments of the small subunit ribosomal RNA gene (SSU rDNA) and the D2-D3 expansion segments of the large subunit ribosomal RNA gene (LSU rDNA D2-D3). In both SSU and LSU phylogenies, all currently sequenced species of Miculenchus formed a monophyletic group with maximal clade support in both Bayesian inference and maximum likelihood analysis.

scholarly journals Five Fungal Pathogens Are Responsible for Bayberry Twig Blight and Fungicides Were Screened for Disease Control

2020 ◽  
Vol 8 (5) ◽  
pp. 689 ◽  
Author(s):  
Wenjun Li ◽  
Ming Hu ◽  
Yang Xue ◽  
Zhijun Li ◽  
Yanfei Zhang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Fungal Pathogens ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Its Region ◽  
Small Subunit ◽  
Field Application ◽  
Financial Loss ◽  
Twig Blight

Bayberry (Myrica rubra) is a commercial fruit in China. For the past seven years, twig blight disease has been attacking bayberry plantations in Shantou City, Guangdong Province, China, leading to destructive damage and financial loss. In this study, five fungal species associated with twig dieback and stem blight were identified based on morphological characteristics combined with multilocus sequence analysis (MLSA) on the internal transcribed spacer (ITS) region, partial sequences of β-tubulin (tub2), translation elongation factor 1-α (tef1-α), large subunit ribosomal RNA (LSU) and small subunit ribosomal RNA (SSU) genes, which are Epicoccum sorghinum, Neofusicoccum parvum, Lasiodiplodia theobromae, Nigrospora oryzae and a Pestalotiopsis new species P. myricae. P. myricae is the chief pathogen in fields, based on its high isolation rate and fast disease progression after inoculation. To our knowledge, this is the first study reporting the above five fungi as the pathogens responsible for bayberry twig blight. Indoor screening of fungicides indicates that Prochloraz (copper salt) is the most promising fungicide for field application, followed by Pyraclostrobin, 15% Difenoconazole + 15% Propiconazole, Difenoconazole and Myclobutanil. Additionally, Bacillus velezensis strain 3–10 and zeamines from Dickeya zeae strain EC1 could be used as potential ecofriendly alternatives to control the disease.

A hidden break in the 28.0S rRNA from Diphyllobothrium dendriticum

1992 ◽  
Vol 66 (3) ◽  
pp. 193-197 ◽  
Author(s):  
K. A. Karlstedt ◽  
G. I. L. Paatero ◽  
J.-H. Mäkelä ◽  
B.-J. Wikgren
Keyword(s):  
Ribosomal Rna ◽  
Northern Blot ◽  
Gel Electrophoresis ◽  
Large Subunit ◽  
Small Subunit ◽  
Agarose Gel ◽  
Oligonucleotide Probes ◽  
Agarose Gel Electrophoresis ◽  
Diphyllobothrium Dendriticum ◽  
Large Subunit Ribosomal Rna

ABSTRACTNondenatured and denatured total RNA from the tapeworm Diphyllobothrium dendriticum (Cestoda) was analysed by agarose gel electrophoresis. It was found that the large subunit ribosomal RNA (lrRNA) is 28.0S and the small subunit ribosomal RNA (srRNA) is 19.5S. Following denaturation the 28.0S rRNA was disrupted into a 19.5S subfragment and a 20.7S subfragment due to the presence of a centrally located hidden break. By hybridization of Northern blot membranes with oligonucleotide probes specific for the 5′- and 3′-ends of the lrRNA respectively, we have shown that the 19.5S sub-fragment is from the 5′-end (the α-subfragment) and the 20.7S subfragment from the 3′-end (the β-subfragment) of the 28.0S rRNA of D. dendriticum.

scholarly journals ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1418 ◽  
Author(s):  
Adam R. Rivers ◽  
Kyle C. Weber ◽  
Terrence G. Gardner ◽  
Shuang Liu ◽  
Shalamar D. Armstrong
Keyword(s):  
Ribosomal Rna ◽  
Large Subunit ◽  
Marker Gene ◽  
Its Region ◽  
Small Subunit ◽  
Sequence Variant ◽  
Ribosomal Rna Gene ◽  
Conserved Regions ◽  
Conserved Genes ◽  
Internally Transcribed Spacer

The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github.

scholarly journals Multi-Gene Phylogeny and Taxonomy of Hydnellum (Bankeraceae, Basidiomycota) from China

2021 ◽  
Vol 7 (10) ◽  
pp. 818
Author(s):  
Yan-Hong Mu ◽  
Jia-Rui Yu ◽  
Ting Cao ◽  
Xiang-Hua Wang ◽  
Hai-Sheng Yuan
Keyword(s):  
New Species ◽  
Rna Polymerase Ii ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Small Subunit ◽  
Phylogenetic Position ◽  
Ribosomal Rna Gene ◽  
Morphological Studies

The genus Hydnellum is an important group of stipitate hydnaceous fungi which can form ectomycorrhiza with many species of woody plants. In recent decades, the frequency and number of basidiocarps observed in China have been declining significantly. So far, however, we know little about the species diversity of Hydnellum in China. In this study, we conducted molecular phylogenetic analyses based on sections of multiple loci, including the large subunit of nuclear ribosomal RNA gene (nLSU), the internal transcribed spacer regions (ITS), the small subunit of nuclear ribosomal RNA gene (SSU) and the second-largest subunit of RNA polymerase II gene (RPB2), as well as morphological studies, of collected samples of Hydnellum from China. We also inferred Maximum Likelihood and Bayesian phylogenies for the order Thelephorales from the dataset of the combined nLSU and ITS. This study has revealed the phylogenetic position of Hydnellum in the order Thelephorales, and phylogenetically confirmed ten major clades in Thelephorales; Twenty-nine taxa are proposed, described or reported, including 10 new subgenera (Hydnellum subgenus Hydnellum, subg. Caesispinosum, subg. Croceum, subg. Inflatum, subg. Rhizomorphum, subg. Scabrosum, subg. Spongiosum, subg. Subindufibulatum, subg. Violaceum and subg. Zonatum), 11 new species (Hydnellum atrorubrum, H. atrospinosum, H. bomiense, H. brunneorubrum, H. fibulatum, H. granulosum, H. inflatum, H. rubidofuscum, H. squamulosum, H. sulcatum and H. yunnanense), 3 newly recorded species (H. caeruleum, H. peckii and H. spongiosipes) and 5 notable specimens (Hydnellum sp 1, H. sp 2, H. sp 3, H. sp 4 and H. sp 5). A classification system based on the morphological characteristics (especially the hyphal structure types) and molecular analyses is proposed to accommodate most species in Hydnellum. The distinguishing characters of the subgenera and the new species with their closely related taxa are discussed. A key to the species of Hydnellum from China is provided.

Description of Ektaphelenchus berbericus n. sp. (Rhabditida: Ektaphelenchinae) from eastern Iran

Nematology ◽  
2016 ◽  
Vol 18 (9) ◽  
pp. 1063-1077 ◽  
Author(s):  
Somaye Alvani ◽  
Esmat Mahdikhani-Moghadam ◽  
Robin M. Giblin-Davis ◽  
Majid Pedram
Keyword(s):  
New Species ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Slight Variation ◽  
Internal Transcribed Spacer Region ◽  
Lateral Field ◽  
Ribosomal Rna Gene ◽  
Eastern Iran

Ektaphelenchus berbericus n. sp. was recovered from soil samples collected in eastern Iran and is described and illustrated based on morphological, morphometric and molecular data. The new species is characterised by having female body 512-691 μm long, lip region separated from rest of body by a shallow depression, lips separated and equally sized, 19-22 μm long stylet with wide lumen and lacking knobs or swellings at its base, cuticle with fine, but distinct transverse annuli and three lines in lateral field, excretory pore located at base of metacorpus (with slight variation in position), reproductive system monodelphic-prodelphic with spheroid and fine sperm cells inside spermatheca in some individuals and short post-vulval uterine sac (PUS), rectum and anus vestigial (invisible in few individuals), conical posterior body end (tail), narrowing at mid-point between anus and rounded tail tip, and males lacking. The new species is typologically similar to species belonging to four genera: Devibursaphelenchus, Ektaphelenchoides, Ektaphelenchus and Seinura, by a combination of morphological characters, e.g., gross morphology of stylet (lacking knobs or swellings at base), morphology of posterior body end (having short conical tail), PUS length, and having a vestigial anus and rectum in most individuals. In molecular phylogenetic analyses using sequences of the partial small subunit of the ribosomal RNA gene (SSU) and the D2-D3 expansion segments of the large subunit (LSU) ribosomal RNA gene, the new species is close to the Ektaphelenchoides/Cryptaphelenchus clade in an inferred SSU tree, and formed a clade with Ektaphelenchoides and Devibursaphelenchus spp. in a D2-D3 LSU tree. Further phylogenetic analyses using full length sequences of the internal transcribed spacer region (ITS) (= ITS1 + 5.8S + ITS2) corroborated results from the SSU and D2-D3 LSU trees, and the multilocus analyses using the combined SSU and LSU data placed the new species in a robustly supported clade with Ektaphelenchoides poinari and Devibursaphelenchus lini.

Parasitodiplogaster species associated with Pharmacosycea figs in Panama

Nematology ◽  
2014 ◽  
Vol 16 (5) ◽  
pp. 607-619 ◽  
Author(s):  
Natsumi Kanzaki ◽  
Robin M. Giblin-Davis ◽  
Weimin Ye ◽  
Edward Allen Herre ◽  
Barbara J. Center
Keyword(s):  
Ribosomal Rna ◽  
Morphological Study ◽  
Large Subunit ◽  
Morphological Characters ◽  
Small Subunit ◽  
Nominal Species ◽  
Monophyletic Clade ◽  
Male Tail ◽  
Stomatal Morphology ◽  
Rna Genes

Parasitodiplogaster species that are associated with figs in the Ficus subsection Pharmacosycea, i.e., Ficus maxima, F. yoponensis, F. insipida and F. glabrata, were studied using morphological characters and molecular sequences. Some nematodes isolated from the fig sycones were casually observed and recorded as morphospecies according to their morphotype, and were then digested for their DNA, while others were fixed in formalin-glycerin for additional morphological study. High resolution microscopic observation of the morphological materials yielded five morphospecies including two nominal species, P. maxinema and P. pharmaconema. The morphospecies were distinguished from each other by male tail characters. By contrast, five and six genotypes were recognised by D2/D3 expansion segments of the large subunit (LSU) and near-full-length sequences of small subunit (SSU) ribosomal RNA genes, respectively. Except for two nominal species, genotypes and morphospecies were not clearly correlated because of limitations in the microscopic resolution in the initial morphotyping. Although the morphospecies and genotypes were not clearly paired, Pharmacosycea-associated Parasitodiplogaster species, which are tentatively referred to as the ‘P. maxinema group’, formed a monophyletic clade in both D2/D3 LSU and SSU analyses and are morphologically characterised by their stomatal morphology, i.e., a tube-shaped stoma with two stick-like teeth and male tail morphology, presence of nine paired papillae and relatively slender spicule.

Description of Ruehmaphelenchus fujiensis n. sp. (Tylenchomorpha: Aphelenchoididae) isolated from dead wood of Quercus crispula from Yamanashi, Japan

Nematology ◽  
2021 ◽  
pp. 1-18
Author(s):  
Natsumi Kanzaki
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Botrytis Cinerea ◽  
Ribosomal Rna ◽  
Dead Wood ◽  
Large Subunit ◽  
Small Subunit ◽  
Quercus Crispula ◽  
Female Tail ◽  
Molecular Phylogenetic

Summary Three undescribed Ruehmaphelenchus species were isolated from dead wood of Quercus crispula collected in three different localities in Japan. One of these three species was successfully cultured using Botrytis cinerea as its food fungus and is described and figured as R. fujiensis n. sp. The new species is characterised by the following features: male tail, conical with or without a projection; female tail, conical with variously shaped terminal mucron or projection; and male spicule possessing a relatively long and triangular condylus. The new species is close to, or almost a cryptic species of R. digitulus, i.e., the typological characters and morphometric values of these two species are mostly overlapping. In a molecular phylogenetic relationship inferred from near-full-length small subunit (18S) and D2-D3 expansion segments of the large subunit (28S) of ribosomal RNA, the new species is close to R. asiaticus, R. digitulus, R. formosanus, and Ruehmaphelenchus sp. NKZ202; however, it was clearly separated from these species.

Bursaphelenchus sakishimanus n. sp. (Tylenchomorpha: Aphelenchoididae) isolated from a stag beetle, Dorcus titanus sakishimanus Nomura (Coleoptera: Lucanidae), on Ishigaki Island, Japan

Nematology ◽  
2015 ◽  
Vol 17 (5) ◽  
pp. 531-542 ◽  
Author(s):  
Natsumi Kanzaki ◽  
Kimiko Okabe ◽  
Youichi Kobori
Keyword(s):  
New Species ◽  
Ribosomal Rna ◽  
Large Subunit ◽  
Agar Plate ◽  
Small Subunit ◽  
Full Length ◽  
Ishigaki Island ◽  
Tropical America ◽  
Stag Beetles ◽  
Close Relatives

An undescribedBursaphelenchusspecies was isolated and cultured fromDorcus titanus sakishimanuscollected during a field survey of the insect-associated nematodes in subtropical Japan. The stag beetles were collected from Ishigaki Island, Okinawa, Japan, and dissected to examine their nematode associates. Then the dissected bodies were individually transferred to 2.0% agar plates, and nematode propagation on the plates was periodically examined. Nematodes were first recovered from the agar plate,i.e., the number of nematodes carried by the beetle was low, and infection was not confirmed during dissection. The new species was morphologically and phylogenetically (on a molecular basis) close toB. gerberae, which was isolated from the palm weevil,Rhynchophorus palmarum(Curculionidae), from tropical America, and to other weevil-associatedBursaphelenchusspecies. However, the new species can be distinguished from its close relatives by its typological characters,e.g., long and slender female tail and male spicule morphology as well as phylogenetic status inferred from the near-full-length of the small subunit (SSU) of the ribosomal RNA gene. The new species is described and illustrated herein asB. sakishimanusn. sp. and its molecular profiles, near-full-length SSU, and D2-D3 expansion segments of the large subunit of ribosomal RNA are described. This is the secondBursaphelenchusspecies associated with stag beetles (Lucanidae).

Description of Ruehmaphelenchus formosanus n. sp. (Tylenchina: Aphelenchoididae) isolated from Euwallacea fornicates from Taiwan

Nematology ◽  
2013 ◽  
Vol 15 (8) ◽  
pp. 895-906 ◽  
Author(s):  
Natsumi Kanzaki ◽  
Hayato Masuya ◽  
Hisatomo Taki ◽  
Kimiko Okabe ◽  
Chi-Yu Chen
Keyword(s):  
New Species ◽  
Phylogenetic Tree ◽  
Ribosomal Rna ◽  
Large Subunit ◽  
Small Subunit ◽  
Ambrosia Beetle ◽  
Biodiversity Survey ◽  
Molecular Phylogenetic Tree ◽  
Molecular Phylogenetic ◽  
Males And Females

A Ruehmaphelenchus species was isolated from an ambrosia beetle, Euwallacea fornicates, during a biodiversity survey of entomophilic nematodes in Taichung, Taiwan. The new species is characterised by a unique tail morphology in both males and females, and a unique spicule morphology in males. The male spicule has clear dorsal and ventral limbs (connected by a blade-like cuticle), a triangular membrane-like structure on its sides, and short, conspicuous, laterally oriented, projections at the distal end. In a molecular phylogenetic tree, inferred from near-full-length small subunit (SSU: 18S) and D2/D3 expansion segments of the large subunit (LSU: 28S) of ribosomal RNA, the new species and other nominal and undescribed Ruehmaphelenchus species formed a well supported clade within Bursaphelenchus. Although this result supports a previous study that suggested that Ruehmaphelenchus is a junior synonym of Bursaphelenchus, the generic relationship between Ruehmaphelenchus and Bursaphelenchus remains somewhat uncertain. Therefore, R. formosanus n. sp. is described as a member of Ruehmaphelenchus, although this should be regarded as a tentative placement.

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