The full-length mitochondrial rDNA sequence of Tyrophagus longior (Astigmata: Acaridae) and phylogeny of astigmatid mites based on mitochondrial rDNA sequences

2017 ◽  
Vol 71 ◽  
pp. 5-13 ◽  
Author(s):  
Banghe Yang ◽  
Chaopin Li
Keyword(s):  
Rdna Sequence ◽  
Full Length ◽  
Rdna Sequences ◽  
Mitochondrial Rdna ◽  
Astigmatid Mites

scholarly journals Unexplored diversity of microscopic myxomycetes: evidence from environmental DNA

2019 ◽  
Vol 152 (3) ◽  
pp. 499-506 ◽  
Author(s):  
Oleg N. Shchepin ◽  
Martin Schnittler ◽  
Nikki H.A. Dagamac ◽  
Dmitry V. Leontyev ◽  
Yuri K. Novozhilov
Keyword(s):  
New Species ◽  
18S Rdna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Environmental Dna ◽  
Full Length ◽  
Detection Techniques ◽  
Rdna Sequences ◽  
18S Rdna Sequences ◽  
Environmental Sequences

Background and aims – Recent studies showed the position of two slime mould species with microscopic sporocarps, Echinosteliopsis oligospora and Echinostelium bisporum, within the class Myxomycetes. These minute species are seldom seen in studies based on detection of sporocarps and can easily be confused with protosteloid amoebozoans.Methods – We searched all published ePCR data sets that targeted myxomycete 18S rDNA for the presence of environmental sequences similar to E. oligospora and Echinosteliales in traditional circumscription, and performed phylogenetic analyses that included short environmental sequences and full-length 18S rDNA sequences representing all the major groups of myxomycetes.Key results – We report 19 unique sequences which are closely related to E. bisporum or E. oligospora based on sequence similarity (73.1–95.2% similarity) and which form well-supported monophyletic clades with these species in phylogenetic analyses. They may represent new species that are not yet described. Our phylogeny based on full-length 18S rDNA sequences further confirms the position of E. bisporum and E. oligospora within myxomycetes and the paraphyly of the order Echinosteliales in its traditional circumscription.Conclusions – Our results show that ePCR-based studies can reveal myxomycete taxa that often escape detection by traditional approaches, including potentially new species, and thus provide valuable new data on diversity and ecology of myxomycetes. As such, strategies for studying myxomycetes biodiversity should be revised, focusing also on molecular detection techniques in addition to the sporocarp-based ones.

scholarly journals Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom Korarchaeota

1998 ◽  
Vol 64 (12) ◽  
pp. 5064-5066 ◽  
Author(s):  
Clifford F. Brunk ◽  
Nicole Eis
Keyword(s):  
Internal Standard ◽  
Pcr Amplification ◽  
Quantitative Measure ◽  
Pcr Primers ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rdna Sequence ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Rdna Sequences

ABSTRACT Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.

A new entomopathogenic nematode, Steinernema colombiense n. sp. (Nematoda: Steinernematidae), from Colombia

Nematology ◽  
2008 ◽  
Vol 10 (4) ◽  
pp. 561-574 ◽  
Author(s):  
Juan Carlos López-Núñez ◽  
Kathryn Plichta ◽  
Carmenza E. Góngora-Botero ◽  
S. Patricia Stock
Keyword(s):  
Excretory Pore ◽  
Sequence Data ◽  
Entomopathogenic Nematode ◽  
Tail Length ◽  
Rdna Sequence ◽  
Its Rdna ◽  
Infective Juvenile ◽  
Diagnostic Features ◽  
Rdna Sequences ◽  
Rdna Sequence Data

Abstract A new entomopathogenic nematode, Steinernema colombiense n. sp., is described from Colombia. Morphological, molecular (28S and ITS rDNA sequence data) and cross-hybridisation studies were used for diagnostics and identification purposes. In addition, 28S and ITS rDNA sequence data were used to assess evolutionary relationships of the new species with other Steinernema spp. Morphological diagnostic features for S. colombiense n. sp. include morphometric features of the third-stage infective juvenile, including body length of 636 (549-732) μm, narrow body diam. (31 (22-36) μm), position of the excretory pore (35 (31-40) μm), tail length (41 (32-53) μm), D% = 29 (25-33) and E% = 205 (138-284). In addition, males of first and second generations are characterised by the morphology of the spicules and gubernaculum, the number and arrangement of the genital papillae and the excretory pore position (at 67 (56-76) and 54 (46-63) μm, for first and second generations, respectively). In addition to these traits, 28S and ITS rDNA sequences analyses both showed this species to be a distinct and unique entity.

Phylogenetic placement of unculturedCeanothusmicrosymbionts using 16S rRNA gene sequences

1999 ◽  
Vol 77 (9) ◽  
pp. 1208-1213 ◽  
Author(s):  
Nancy J Ritchie ◽  
David D Myrold
Keyword(s):  
16S Rdna ◽  
Phylogenetic Trees ◽  
Full Length ◽  
Likelihood Method ◽  
Rrna Gene ◽  
Consensus Sequences ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Polymerase Chain ◽  
Ceanothus Americanus

Full-length 16S rDNA sequences were amplified directly from the nodules of Ceanothus americanus L. and Ceanothus thyrsiflorus Eschsch. using the polymerase chain reaction. Sequences were determined using an automated sequencer, compared against those in GenBank, and assembled into consensus sequences. The sequences were aligned with other full-length Frankia 16S rDNA sequences available from the data base. Phylogenetic trees were obtained using three different algorithms: neighbor joining, parsimony, and the maximum-likelihood method. All three methods showed that these Ceanothus L. microsymbionts were most closely related to the microsymbiont associated with Dryas drummondii Richardson ex Hook. Lvs. rather than Frankia isolated from the Elaeagnaceae.Key words: Frankia, Ceanothus, 16S rDNA.

Systematics and biogeography of Rhodniini (Heteroptera: Reduviidae: Triatominae) based on 16S mitochondrial rDNA sequences

2007 ◽  
Vol 34 (4) ◽  
pp. 699-712 ◽  
Author(s):  
Alexandre Silva de Paula ◽  
Liléia Diotaiuti ◽  
Cleber Galvão
Keyword(s):  
Rdna Sequences ◽  
Mitochondrial Rdna

Micarea soralifera sp. nov., a new sorediate species in the M. prasina group

2016 ◽  
Vol 48 (3) ◽  
pp. 161-169 ◽  
Author(s):  
Beata GUZOW-KRZEMIŃSKA ◽  
Paweł CZARNOTA ◽  
Anna ŁUBEK ◽  
Martin KUKWA
Keyword(s):  
Phylogenetic Analyses ◽  
Rdna Sequence ◽  
Its Rdna ◽  
Rdna Sequences

AbstractMicarea soralifera sp. nov., a new sorediate species belonging to the M. prasina group, is characterized by soralia developing directly from the endoxylic thallus or small external areoles, as well as the presence of micareic acid. Phylogenetic analyses of mtSSU rDNA sequences have shown that its closest relative is M. subviridescens. ITS rDNA sequence, a marker proposed as the universal barcoding region of fungi, was generated from the holotype.

scholarly journals Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium

2004 ◽  
Vol 54 (3) ◽  
pp. 851-855 ◽  
Author(s):  
Wan-Taek Im ◽  
Hee-Sung Bae ◽  
Akira Yokota ◽  
Sung Taik Lee
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Rdna Sequence ◽  
The Novel ◽  
Comamonas Testosteroni ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
Degrading Bacterium ◽  
16S Rdna Sequences ◽  
Type Strains

A 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of Comamonas testosteroni, was reclassified as a member of the genus Herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16S rDNA sequences. Phylogenetic inference based on 16S rDNA sequences showed that strain CPW301T clusters in a phylogenetic branch that contains Herbaspirillum species. 16S rDNA sequence similarity of strain CPW301T to species of the genus Herbaspirillum with validly published names is in the range 98·7–98·9 %. Despite the considerably high 16S rDNA sequence similarity, strain CPW301T could be distinguished clearly from type strains of Herbaspirillum species with validly published names by DNA–DNA relatedness values, which were <15·7 %. The genomic DNA G+C content of strain CPW301T is 61·3 mol%. The predominant ubiquinone is Q-8 and the major cellular fatty acids are C16 : 0 and cyclo-C17 : 0. The strain does not fix nitrogen and is not plant-associated. It is an aerobic rod with one unipolar flagellum. On the basis of these characteristics, a novel Herbaspirillum species, Herbaspirillum chlorophenolicum sp. nov., is proposed. The type strain of the novel species is strain CPW301T (=KCTC 12096T=IAM 15024T).

scholarly journals Plastome variation and phylogeny of Taxillus (Loranthaceae)

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256345
Author(s):  
Huei-Jiun Su ◽  
Shu-ling Liang ◽  
Daniel L. Nickrent
Keyword(s):  
Nadh Dehydrogenase ◽  
General Pattern ◽  
Trna Genes ◽  
Dna Barcodes ◽  
Variable Regions ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
Difficult Genus ◽  
Molecular Phylogenetic ◽  
Mitochondrial Rdna

Several molecular phylogenetic studies of the mistletoe family Loranthaceae have been published such that now the general pattern of relationships among the genera and their biogeographic histories are understood. Less is known about species relationships in the larger (> 10 species) genera. This study examines the taxonomically difficult genus Taxillus composed of 35–40 Asian species. The goal was to explore the genetic diversity present in Taxillus plastomes, locate genetically variable hotspots, and test these for their utility as potential DNA barcodes. Using genome skimming, complete plastomes, as well as nuclear and mitochondrial rDNA sequences, were newly generated for eight species. The plastome sequences were used in conjunction with seven publicly available Taxillus sequences and three sequences of Scurrula, a close generic relative. The Taxillus plastomes ranged from 121 to 123 kbp and encoded 90–93 plastid genes. In addition to all of the NADH dehydrogenase complex genes, four ribosomal genes, infA and four intron-containing tRNA genes were lost or pseudogenized in all of the Taxillus and Scurrula plastomes. The topologies of the plastome, mitochondrial rDNA and nuclear rDNA trees were generally congruent, though with discordance at the position of T. chinensis. Several variable regions in the plastomes were identified that have sufficient numbers of parsimony informative sites as to recover the major clades seen in the complete plastome tree. Instead of generating complete plastome sequences, our study showed that accD alone or the concatenation of accD and rbcL can be used in future studies to facilitate identification of Taxillus samples and to generate a molecular phylogeny with robust sampling within the genus.

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