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intergenic spacer region

Madhavi L Kakumanu, Loganathan Ponnusamy, Haley Sutton, Steven R Meshnick, William L Nicholson, Charles S Apperson
The American dog tick, Dermacentor variabilis (Say), is a vector of spotted fever group (SFG) rickettsiae, including Rickettsia rickettsii the causative organism of Rocky Mountain spotted fever (RMSF). In North Carolina, SFG rickettsioses (including RMSF) are a leading cause of tick-borne illness. Knowledge of the infection rate and geographic distribution of D. variabilis ticks infected with Rickettsia spp. provides information on the spatial distribution of public health risk. Accordingly, we extracted genomic DNA from adult D...
May 16, 2018: Journal of Medical Entomology
Osama Sammra, Jörg Rau, Jörn Wickhorst, Mazen Alssahen, Abdulwahed Ahmed Hassan, Christoph Lämmler, Ellen Prenger-Berninghoff, Amir Abdulmawjood
The newly described type strains Arcanobacterium pinnipediorum DSM 28752T and Arcanobacterium wilhelmae DSM 102162T , initially isolated from an anal swab of a harbor seal (Sammra et al. Int J Syst Evol Microbiol 65:4539-4543, 2015) and the genital tract of a rhinoceros (Sammra et al. Int J Syst Evol Microbiol 67:2093-2097, 2017), could be further characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and Fourier transform infrared (FT-IR) spectroscopy and by sequencing the genomic targets 16S-23S rDNA intergenic spacer region (ISR) and the genes rpoB, gap, and tuf...
May 13, 2018: Folia Microbiologica
Qing Zhao, Juan Wang, Meng-Qing Wang, Bo Cai, Hu-Fang Zhang, Jiu-Feng Wei
Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) is used as a biological control agent against various insect pests for its predatory. In the present study, the complete mitochondrial genome (mitogenome) of the species was sequenced using the next-generation sequencing technology. The results showed that the mitogenome is 15,952 bp long, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a control region. Furthermore, the gene order and orientation of this mitogenome are identical to those of most heteropterans...
March 1, 2018: Journal of Insect Science
Ali Amiryousefi, Jaakko Hyvönen, Péter Poczai
Bittersweet (Solanum dulcamara) is a native Old World member of the nightshade family. This European diploid species can be found from marshlands to high mountainous regions and it is a common weed that serves as an alternative host and source of resistance genes against plant pathogens such as late blight (Phytophthora infestans). We sequenced the complete chloroplast genome of bittersweet, which is 155,580 bp in length and it is characterized by a typical quadripartite structure composed of a large (85,901 bp) and small (18,449 bp) single-copy region interspersed by two identical inverted repeats (25,615 bp)...
2018: PloS One
Murielle Simo-Droissart, Gregory M Plunkett, Vincent Droissart, Molly B Edwards, João N M Farminhão, Vladimir Ječmenica, Tania D'haijère, Porter P Lowry, Bonaventure Sonké, Claire Micheneau, Barbara S Carlsward, Laura Azandi, Simon Verlynde, Olivier J Hardy, Florent Martos, Benny Bytebier, Eberhard Fischer, Tariq Stévart
Despite significant progress made in recent years toward developing an infrafamilial classification of Orchidaceae, our understanding of relationships among and within tribal and subtribal groups of epidendroid orchids remains incomplete. To reassess generic delimitation among one group of these epidendroids, the African angraecoids, phylogenetic relationships were inferred from DNA sequence data from three regions, ITS, matK, and the trnL-trnF intergenic spacer, obtained from a broadly representative sample of taxa...
April 16, 2018: Molecular Phylogenetics and Evolution
Yuliya Sabitova, Nataliya Fomenko, Artem Tikunov, Oleg Stronin, Maxim Khasnatinov, Davaajav Abmed, Galina Danchinova, Irina Golovljova, Nina Tikunova
Lyme borreliosis (LB) is the most frequently recorded tick-transmitted disease in Eurasia. Tomsk Province, Western Siberia in Russia and Selenge Aimag in Northern Mongolia are leading regions in the LB incidence rate in these countries. Spirochaetes of the Borrelia burgdorferi sensu lato (s.l.) complex isolated from Ixodes ticks from Tomsk Province (n = 56) and Ixodes persulcatus ticks from Selenge Aimag (n = 5) were genetically characterized using Multi Locus Sequence Typing (MLST), analysis of the 5S23S rRNA intergenic spacer (IGS) amplicons, and p83/100 gene sequencing...
April 13, 2018: Infection, Genetics and Evolution
Eduardo J Boeri, María M Wanke, María J Madariaga, María L Teijeiro, Sebastian A Elena, Marcos D Trangoni
Aim: This study aimed to compare the sensitivity (S), specificity (Sp), and positive likelihood ratios (LR+) of four polymerase chain reaction (PCR) assays for the detection of Brucella spp. in dog's clinical samples. Materials and Methods: A total of 595 samples of whole blood, urine, and genital fluids were evaluated between October 2014 and November 2016. To compare PCR assays, the gold standard was defined using a combination of different serological and microbiological test...
February 2018: Veterinary World
Xia Liu, Yuan Li, Hongyuan Yang, Boyang Zhou
The complete chloroplast (cp) genome of Talinum paniculatum (Caryophyllale), a source of pharmaceutical efficacy similar to ginseng, and a widely distributed and planted edible vegetable, were sequenced and analyzed. The cp genome size of T. paniculatum is 156,929 bp, with a pair of inverted repeats (IRs) of 25,751 bp separated by a large single copy (LSC) region of 86,898 bp and a small single copy (SSC) region of 18,529 bp. The genome contains 83 protein-coding genes, 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes and four pseudogenes...
April 9, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Marta Cegłowska, Anna Toruńska-Sitarz, Grażyna Kowalewska, Hanna Mazur-Marzec
In the Baltic Sea, diazotrophic cyanobacteria have been present for thousands of years, over the whole brackish water phase of the ecosystem. However, our knowledge about the species composition of the cyanobacterial community is limited to the last several decades. In the current study, the presence of species-specific chemical and genetic markers in deep sediments were analyzed to increase the existing knowledge on the history of toxic Nodularia spumigena blooms in the Baltic Sea. As chemical markers, three cyclic nonribosomal peptides were applied: the hepatotoxic nodularin, which in the sea was detected solely in N...
April 4, 2018: Marine Drugs
Rubén Damián Elías-Román, Rosario Medel-Ortiz, Dionicio Alvarado-Rosales, John W Hanna, Amy L Ross-Davis, Mee-Sook Kim, Ned B Klopfenstein
Armillaria mexicana (Agaricales, Physalacriaceae) is described as a new species based on morphology, DNA sequence data, and phylogenetic analyses. It clearly differs from previously reported Armillaria species in North, Central, and South America. It is characterized by the absence of fibulae in the basidioma, abundant cheilocystidia, and ellipsoidal, hyaline basidiospores that are apparently smooth under light microscope, but slightly to moderately rugulose under scanning electron microscope. It is differentiated from other Armillaria species by macromorphological characters, including annulus structure, pileus and stipe coloration, and other structures...
January 19, 2018: Mycologia
Wencai Wang, Siyun Chen, Xianzhi Zhang
Eucommia ulmoides ( E. ulmoides ), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of E. ulmoides lags far behind largely due to the scarcity of genomic data. In this study, one complete chloroplast (cp) genome of E. ulmoides was generated via the genome skimming approach and compared to another available E. ulmoides cp genome comprehensively at the genome scale. We found that the structure of the cp genome in E...
March 30, 2018: International Journal of Molecular Sciences
Sajjad Asaf, Abdul Latif Khan, Muhammad Aaqil Khan, Raheem Shahzad, Lubna, Sang Mo Kang, Ahmed Al-Harrasi, Ahmed Al-Rawahi, In-Jung Lee
Pinaceae, the largest family of conifers, has a diversified organization of chloroplast (cp) genomes with two typical highly reduced inverted repeats (IRs). In the current study, we determined the complete sequence of the cp genome of an economically and ecologically important conifer tree, the loblolly pine (Pinus taeda L.), using Illumina paired-end sequencing and compared the sequence with those of other pine species. The results revealed a genome size of 121,531 base pairs (bp) containing a pair of 830-bp IR regions, distinguished by a small single copy (42,258 bp) and large single copy (77,614 bp) region...
2018: PloS One
Priyanka Mishra, Ashutosh K Shukla, Velusamy Sundaresan
Senna alexandrina (Fabaceae) is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes ( rbcL and matK ) and intergenic spacers ( psbA-trnH and ITS ) were developed for S...
2018: Frontiers in Plant Science
Francesco Cicala, James D Moore, Jorge Cáceres-Martínez, Miguel A Del Río-Portilla, Mónica Hernández-Rodríguez, Rebeca Vásquez-Yeomans, Axayácatl Rocha-Olivares
Withering syndrome (WS) is a chronic wasting disease affecting abalone species attributed to the pathogen Candidatus Xenohaliotis californiensis (CXc). Wild populations of blue (Haliotis fulgens) and yellow (H. corrugata) abalone have experienced unusual mortality rates since 2009 off the peninsula of Baja California and WS has been hypothesized as a possible cause. Currently, little information is available about the genetic diversity of CXc and particularly the possible existence of strains differing in pathogenicity...
March 22, 2018: Journal of Invertebrate Pathology
Brandon T Sinn, Dylan D Sedmak, Lawrence M Kelly, John V Freudenstein
PREMISE OF THE STUDY: As more plastomes are assembled, it is evident that rearrangements, losses, intergenic spacer expansion and contraction, and syntenic breaks within otherwise functioning plastids are more common than was thought previously, and such changes have developed independently in disparate lineages. However, to date, the magnoliids remain characterized by their highly conserved plastid genomes (plastomes). METHODS: Illumina HiSeq and MiSeq platforms were used to sequence the plastomes of Saruma henryi and those of representative species from each of the six taxonomic sections of Asarum...
January 2018: American Journal of Botany
Xiaofeng Chi, Jiuli Wang, Qingbo Gao, Faqi Zhang, Shilong Chen
The genus Lancea is native to the Qinghai-Tibetan Plateau and consists of two species, Lancea tibetica Hook. f. et Thoms. and Lancea hirsuta Bonati. Here, we report the complete sequences of the chloroplast genomes of L. tibetica and L. hirsuta , which were 153,665 and 154,045 bp in length, respectively, and each included a pair of inverted repeated regions (25,624 and 25,838 bp in length, respectively) that were separated by a large single copy region (84,401 and 84,588 bp in length, respectively) and a smaller single copy region (18,016 and 17,781 bp in length, respectively)...
March 7, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Cécile Revellin, Alain Hartmann, Sébastien Solanas, Edward Topp
Antibiotics are entrained in agricultural soil through the application of manures from medicated animals. In the present study, a series of small field plots was established in 1999 that receive annual spring applications of a mixture of tylosin, sulfamethazine, and chlortetracycline at concentrations ranging from 0.1 to 10 mg · kg-1 soil. These antibiotics are commonly used in commercial swine production. The field plots were cropped continuously for soybeans, and in 2012, after 14 annual antibiotic applications, the nodules from soybean roots were sampled and the occupying bradyrhizobia were characterized...
May 1, 2018: Applied and Environmental Microbiology
Jianguo Zhou, Yingxian Cui, Xinlian Chen, Ying Li, Zhichao Xu, Baozhong Duan, Yonghua Li, Jingyuan Song, Hui Yao
Papaver rhoeas L. and P. orientale L., which belong to the family Papaveraceae, are used as ornamental and medicinal plants. The chloroplast genome has been used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of P. rhoeas and P. orientale are reported. Results show that the complete chloroplast genomes of P. rhoeas and P. orientale have typical quadripartite structures, which are comprised of circular 152,905 and 152,799-bp-long molecules, respectively...
February 16, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
J E Moore, J Hirayama, K Hayashi, C Mason, W Coulter, M Matsuda, C E Goldsmith
No abstract text is available yet for this article.
April 2018: British Journal of Biomedical Science
Andrei Stefan, Jannick Van Cauwenberghe, Craita M Rosu, Catalina Stedel, Nikolaos E Labrou, Emmanouil Flemetakis, Rodica C Efrose
The identification and conservation of indigenous rhizobia associated with legume plants and their application as biofertilizers is becoming an agricultural worldwide priority. However, little is known about the genetic diversity and phylogeny of rhizobia in Romania. In the present study, the genetic diversity and population composition of Rhizobium leguminosarum symbiovar trifolii isolates from 12 clover plants populations located across two regions in Romania were analyzed. Red clover isolates were phenotypically evaluated and genotyped by sequencing 16S rRNA gene, 16S-23S intergenic spacer, three chromosomal genes (atpD, glnII and recA) and two plasmid genes (nifH and nodA)...
May 2018: Systematic and Applied Microbiology
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