scholarly journals How Diverse Is the Genus Wolbachia? Multiple-Gene Sequencing Reveals a Putatively New Wolbachia Supergroup Recovered from Spider Mites (Acari: Tetranychidae)

2008 ◽  
Vol 75 (4) ◽  
pp. 1036-1043 ◽  
Author(s):  
Vera I. D. Ros ◽  
Vicki M. Fleming ◽  
Edward J. Feil ◽  
Johannes A. J. Breeuwer
Keyword(s):  
Spider Mite ◽  
Sequence Data ◽  
Nematode Species ◽  
Mite Species ◽  
Rrna Gene ◽  
Protein Coding ◽  
Nucleotide Sequence Data ◽  
Multiple Gene ◽  
Wide Range ◽  
The 16S Rrna Gene

ABSTRACT At least 20% of all arthropods and some nematode species are infected with intracellular bacteria of the genus Wolbachia. This highly diverse genus has been subdivided into eight “supergroups” (A to H) on the basis of nucleotide sequence data. Here, we report the discovery of a new Wolbachia supergroup recovered from the spider mite species Bryobia species V (Acari: Tetranychidae), based on the sequences of three protein-coding genes (ftsZ, gltA, and groEL) and the 16S rRNA gene. Other tetranychid mites possess supergroup B Wolbachia strains. The discovery of another Wolbachia supergroup expands the known diversity of Wolbachia and emphasizes the high variability of the genus. Our data also clarify the existing supergroup structure and highlight the use of multiple gene sequences for robust phylogenetic analysis. In addition to previous reports of recombination between the arthropod-infecting supergroups A and B, we provide evidence for recombination between the nematode-infecting supergroups C and D. Robust delineation of supergroups is essential for understanding the origin and spread of this common reproductive parasite and for unraveling mechanisms of host adaptation and manipulation across a wide range of hosts.

scholarly journals Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.

2004 ◽  
Vol 54 (5) ◽  
pp. 1591-1599 ◽  
Author(s):  
Dawn E. Holmes ◽  
Kelly P. Nevin ◽  
Derek R. Lovley
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Protein Coding ◽  
Subsurface Environments ◽  
The Family ◽  
Conserved Genes ◽  
The 16S Rrna Gene

The sequences of five conserved genes, in addition to the 16S rRNA gene, were investigated in 30 members of the Geobacteraceae fam. nov. All members of the Geobacteraceae examined contained nifD, suggesting that they are capable of nitrogen fixation, which may explain their ability to compete effectively in nitrogen-poor subsurface environments undergoing remediation for petroleum or metal contamination. The phylogenies predicted from rpoB, gyrB, fusA, recA and nifD were generally in agreement with the phylogeny predicted from 16S rRNA gene sequences. Furthermore, phylogenetic analysis of concatemers constructed from all five protein-coding genes corresponded closely with the 16S rRNA gene-based phylogeny. This study demonstrated that the Geobacteraceae is a phylogenetically coherent family within the δ-subclass of the Proteobacteria that is composed of three distinct phylogenetic clusters: Geobacter, Desulfuromonas and Desulfuromusa. The sequence data provided here will make it possible to discriminate better between physiologically distinct members of the Geobacteraceae, such as Pelobacter propionicus and Geobacter species, in geobacteraceae-dominated microbial communities and greatly expands the potential to identify geobacteraceae sequences in libraries of environmental genomic DNA.

scholarly journals PCR-based Specific Detection of Bacillus in Liquid Organic Fertilizer

2019 ◽  
Vol 1 (1) ◽  
pp. 44-47
Author(s):  
Iman Hidayat ◽  
Nur Laili ◽  
Dwi Agustiyani ◽  
Sarjiya Antonius
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Organic Fertilizer ◽  
Bacillus Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Pcr Assay ◽  
Nucleotide Sequence Data ◽  
The 16S Rrna Gene

Rapid molecular PCR-based detection method for Bacillus species used in the production of Beyonic® liquid organic fertilizer was carried out based on nucleotide sequence data from the 16S rRNA gene. The method involved sequencing the 16S rRNA gene of several Bacillus species and identifying around 16-22 specific nucleotide bases from 5' and 3' ends in the Bacillus 16S rRNA gene sequences. One specific primer pair for Bacillus detection was determined as follow: 5' - CAT AAG ACT GGG ATA ACT CCG GG - 3' (forward) from positions of 85-107 bp, and 5’ - CCA GGC GGA GTG CTT AAT GC - 3’ (reverse) from positions of 836-854 bp. PCR assay and gel electrophoresis analysis showed that the primer pair was specific to the genus Bacillus.

scholarly journals GenePiper, a Graphical User Interface Tool for Microbiome Sequence Data Mining

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
W. M. Tong ◽  
Yuki Chan
Keyword(s):  
Graphical User Interface ◽  
Sequence Data ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Wide Range ◽  
R Shiny ◽  
Microbiome Data ◽  
The 16S Rrna Gene ◽  
Graphical User Interface Tool ◽  
Shiny Application

Amplicon sequencing of the 16S rRNA gene is commonly performed for the assessment and comparison of microbiomes. Here, we introduce GenePiper, an open-source R Shiny application that provides an easy-to-use interface, a wide range of analytical methods, and optimized graphical outputs for offline microbiome data analyses.

Photobacterium arenosum sp. nov., isolated from marine sediment sand

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Veeraya Weerawongwiwat ◽  
Seokmin Yoon ◽  
Jong-Hwa Kim ◽  
Jung-Hoon Yoon ◽  
Jung Sook Lee ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Protein Coding ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
The Republic ◽  
The 16S Rrna Gene

A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568T, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25–30 °C, at pH 6.5–8.5 and with 0–4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568T was a member of the genus Photobacterium with high similarity to Photobacterium salinisoli JCM 30852T (97.7 %), Photobacterium halotolerans KACC 17089T (97.3 %) and Photobacterium galatheae LMG F28894T (97.3 %). The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568T was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568T as representing a novel Photobacterium species, for which the name Photobacterium arenosum sp. nov. is proposed. The type strain of this novel species is CAU 1568T (=KCTC 82404T=MCCC 1K05668T).

A new species of Puddle Frog, genus Phrynobatrachus (Amphibia: Anura: Phrynobatrachidae) from Ghana

Zootaxa ◽  
2018 ◽  
Vol 4374 (4) ◽  
pp. 565 ◽  
Author(s):  
CALEB OFORI-BOATENG ◽  
ADAM D. LEACHÉ ◽  
BRIGHT OBENG-KANKAM ◽  
N’GORAN GERMAIN KOUAMÉ ◽  
ANNIKA HILLERS ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New Species ◽  
Sequence Data ◽  
Face Mask ◽  
West African ◽  
Rrna Gene ◽  
Forest Region ◽  
Mtdna Sequence ◽  
A New Species ◽  
The 16S Rrna Gene

We describe a new species of Phrynobatrachus from the eastern part of the Upper Guinea forest region, Ghana, West Africa. Morphologically, the new species can be distinguished from all of its congeners by the combination of a slender body, short and pointed snout, a relatively warty dorsum, a black-spotted throat in both sexes, a gular flap in males, a dark spotted chest, a white-greyish venter with occasional blackish spots, rudimentary pedal webbing, none to slightly dilated finger tips and strongly delated toe tips, presence of both inner and outer metatarsal tubercles and absence of a dark face mask, eyelid tubercles and longer dorsal ridges. We collected mitochondrial DNA (mtDNA) sequence data from the 16S rRNA gene to measure the genetic diversity of the new species, and to estimate phylogenetic relationships. The new species is a distinct and monophyletic evolutionary lineage most closely related to Phrynobatrachus gutturosus, P. fraterculus and P. maculiventris. The discovery of this new species highlights that the biodiversity of West African forests is still incompletely known and that the few remaining forests need urgent protection. 

scholarly journals Three novel lineages of ‘Candidatus Liberibacter africanus’ associated with native rutaceous hosts of Trioza erytreae in South Africa

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 723-731 ◽  
Author(s):  
Ronel Roberts ◽  
Emma T. Steenkamp ◽  
Gerhard Pietersen
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Nucleotide Sequence Data ◽  
Trioza Erytreae

Greening disease of citrus in South Africa is associated with ‘Candidatus Liberibacter africanus’ (Laf), a phloem-limited bacterium vectored by the sap-sucking insect Trioza erytreae (Triozidae). Despite the implementation of control strategies, this disease remains problematic, suggesting the existence of reservoir hosts to Laf. The current study aimed to identify such hosts. Samples from 234 trees of Clausena anisata, 289 trees of Vepris lanceolata and 231 trees of Zanthoxylum capense were collected throughout the natural distribution of these trees in South Africa. Total DNA was extracted from samples and tested for the presence of liberibacters by a generic Liberibacter TaqMan real-time PCR assay. Liberibacters present in positive samples were characterized by amplifying and sequencing rplJ, omp and 16S rRNA gene regions. The identity of tree host species from which liberibacter sequences were obtained was verified by sequencing host rbcL genes. Of the trees tested, 33 specimens of Clausena, 17 specimens of Vepris and 10 specimens of Zanthoxylum tested positive for liberibacter. None of the samples contained typical citrus-infecting Laf sequences. Phylogenetic analysis of 16S rRNA gene sequences indicated that the liberibacters obtained from Vepris and Clausena had 16S rRNA gene sequences identical to that of ‘Candidatus Liberibacter africanus subsp. capensis’ (LafC), whereas those from Zanthoxylum species grouped separately. Phylogenetic analysis of the rplJ and omp gene regions revealed unique clusters for liberibacters associated with each tree species. We propose the following names for these novel liberibacters: ‘Candidatus Liberibacter africanus subsp. clausenae’ (LafCl), ‘Candidatus Liberibacter africanus subsp. vepridis’ (LafV) and ‘Candidatus Liberibacter africanus subsp. zanthoxyli’ (LafZ). This study did not find any natural hosts of Laf associated with greening of citrus. While native citrus relatives were shown to be infected with Laf-related liberibacters, nucleotide sequence data suggest that these are not alternative sources of Laf to citrus orchards, per se.

Hymenobacter Taeanensis Sp. Nov., Radiation Resistant Bacterium Isolated from Coastal Sand Dune

2021 ◽  
Author(s):  
Ji Hee Lee ◽  
Jong-Hyun Jung ◽  
Min-Kyu Kim ◽  
Han Na Choe ◽  
Sangyong Lim
Keyword(s):  
Gamma Radiation ◽  
Sand Dune ◽  
Rrna Gene ◽  
Sand Sample ◽  
Coastal Sand Dune ◽  
Respiratory Quinone ◽  
Protein Coding ◽  
Radiation Resistant ◽  
Coastal Sand ◽  
The 16S Rrna Gene

Abstract An aerobic, Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, and light pink-colored bacterial strain, designated TS19T, was isolated from a sand sample obtained from a coastal sand dune after exposure to 3 kGy of gamma radiation. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the isolate was a member of the genus Hymenobacter and was most closely related to H. wooponensis WM78T (98.3% similarity). Strain TS19T and H. wooponensis showed resistance to gamma radiation with D10 values (i.e., the dose required to reduce the bacterial population by tenfold) of 7.3 kGy and 3.5 kGy, respectively. The genome of strain TS19T consists of one contig with 4,879,662 bp and has a G+C content of 56.2%. The genome contains 3,955 protein coding sequences, 44 tRNAs, and 12 rRNAs. The predominant fatty acids of strain TS19T were iso-C15:0, summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B), summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), and C16:1 ω5c. The major polar lipids were phosphatidylethanolamine, and one unknown aminophospholipid. The main respiratory quinone was menaquinone-7. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain TS19T represents a novel species, for which the name Hymenobacter taeanensis sp. nov. is proposed. The type strain is TS19T (=KCTC 72897T =JCM 34023T).

The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism

Parasitology ◽  
2011 ◽  
Vol 138 (13) ◽  
pp. 1760-1777 ◽  
Author(s):  
LAURA M. McDONAGH ◽  
JAMIE R. STEVENS
Keyword(s):  
Sequence Data ◽  
Single Gene ◽  
Nuclear Gene ◽  
Evolutionary Status ◽  
28S Rrna ◽  
Gene Trees ◽  
Data Set ◽  
Protein Coding ◽  
Nucleotide Sequence Data ◽  
The Family

SUMMARYThe Calliphoridae include some of the most economically significant myiasis-causing flies in the world – blowflies and screwworm flies – with many being notorious for their parasitism of livestock. However, despite more than 50 years of research, key taxonomic relationships within the family remain unresolved. This study utilizes nucleotide sequence data from the protein-coding genes COX1 (mitochondrial) and EF1α (nuclear), and the 28S rRNA (nuclear) gene, from 57 blowfly taxa to improve resolution of key evolutionary relationships within the family Calliphoridae. Bayesian phylogenetic inference was carried out for each single-gene data set, demonstrating significant topological difference between the three gene trees. Nevertheless, all gene trees supported a Calliphorinae-Luciliinae subfamily sister-lineage, with respect to Chrysomyinae. In addition, this study also elucidates the taxonomic and evolutionary status of several less well-studied groups, including the genus Bengalia (either within Calliphoridae or as a separate sister-family), genus Onesia (as a sister-genera to, or sub-genera within, Calliphora), genus Dyscritomyia and Lucilia bufonivora, a specialised parasite of frogs and toads. The occurrence of cross-species hybridisation within Calliphoridae is also further explored, focusing on the two economically significant species Lucilia cuprina and Lucilia sericata. In summary, this study represents the most comprehensive molecular phylogenetic analysis of family Calliphoridae undertaken to date.

Variation in the microbiome of the spider mite Tetranychus truncatus with sex, instar and endosymbiont infection

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Yu-Xi Zhu ◽  
Zhang-Rong Song ◽  
Shi-Mei Huo ◽  
Kun Yang ◽  
Xiao-Yue Hong
Keyword(s):  
Spider Mite ◽  
Potential Role ◽  
Developmental Stages ◽  
Spider Mites ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Operational Taxonomic Units ◽  
Dominant Bacteria ◽  
The 16S Rrna Gene

ABSTRACT Most arthropod-associated bacterial communities play a crucial role in host functional traits, whose structure could be dominated by endosymbionts. The spider mite Tetranychus truncatus is a notorious agricultural pest harboring various endosymbionts, yet the effects of endosymbionts on spider mite microbiota remain largely unknown. Here, using deep sequencing of the 16S rRNA gene, we characterized the microbiota of male and female T. truncatus with different endosymbionts (Wolbachia and Spiroplasma) across different developmental stages. Although the spider mite microbiota composition varied across the different developmental stages, Proteobacteria were the most dominant bacteria harbored in all samples. Positive relationships among related operational taxonomic units dominated the significant coassociation networks among bacteria. Moreover, the spider mites coinfected with Wolbachia and Spiroplasma had a significantly higher daily fecundity and juvenile survival rate than the singly infected or uninfected spider mites. The possible function of spider-mite associated bacteria was discussed. Our results highlight the dynamics of spider mite microbiotas across different life stages, and the potential role of endosymbionts in shaping the microbiota of spider mites and improving host fitness.

Molecular identification ofSarcocystisspp. helped to define the origin of green pythons (Morelia viridis) confiscated in Germany

Parasitology ◽  
2013 ◽  
Vol 141 (5) ◽  
pp. 646-651 ◽  
Author(s):  
GASTÓN MORÉ ◽  
NIKOLA PANTCHEV ◽  
DALAND C. HERRMANN ◽  
MAJDA GLOBOKAR VRHOVEC ◽  
SABINE ÖFNER ◽  
...  
Keyword(s):  
18S Rrna ◽  
Sequence Data ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Intermediate Hosts ◽  
Apicomplexan Parasites ◽  
Large Numbers ◽  
Wide Range ◽  
18S Rrna Genes

SUMMARYSarcocystisspp. represent apicomplexan parasites. They usually have a heteroxenous life cycle. Around 200 species have been described, affecting a wide range of animals worldwide, including reptiles. In recent years, large numbers of reptiles have been imported into Europe as pets and, as a consequence, animal welfare and species protection issues emerged. A sample of pooled feces from four confiscated green pythons (Morelia viridis) containingSarcocystisspp. sporocysts was investigated. These snakes were imported for the pet trade and declared as being captive-bred. Full length 18S rRNA genes were amplified, cloned into plasmids and sequenced. Two differentSarcocystisspp. sequences were identified and registered asSarcocystissp. fromM. viridisin GenBank. Both showed a 95–97% sequence identity with the 18S rRNA gene ofSarcocystis singaporensis.Phylogenetic analysis positioned these sequences together with otherSarcocystisspp. from snakes and rodents as definitive and intermediate hosts (IH), respectively. Sequence data and also the results of clinical and parasitological examinations suggest that the snakes were definitive hosts forSarcocystisspp. that circulate in wild IH. Thus, it seems unlikely that the infected snakes had been legally bred. Our research shows that information on the infection of snakes withSarcocystisspp. may be used to assess compliance with regulations on the trade with wildlife species.

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