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intergenic spacer region

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https://www.readbyqxmd.com/read/28437593/tabula-rasa-in-the-patagonian-channels-the-phylogeography-of-oreobolus-obtusangulus-cyperaceae
#1
Simon Pfanzelt, Dirk C Albach, Klaus Bernhard von Hagen
The extent of the Pleistocene glaciations in the Patagonian Channel region (southwesternmost South America) and their impact on the vegetation there is largely unknown. Whether the regional flora was wiped out completely (tabula rasa) or survived in ice-free pockets (in situ survival) is still an open question. The molecular imprint of either scenario should still be visible in extant populations. Therefore, DNA sequence data of Oreobolus obtusangulus Gaudich. (Cyperaceae) were analyzed. This species is an abundant constitutent of Patagonian cushion peat bogs, one of the Patagonian Channel region's major vegetation types...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28435087/the-complete-mitochondrial-genome-of-clostera-anachoreta-lepidoptera-notodontidae-and-phylogenetic-implications-for-noctuoidea-species
#2
Xiao-Yu Zhu, Zhao-Zhe Xin, Ying Wang, Hua-Bin Zhang, Dai-Zhen Zhang, Zheng-Fei Wang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
In this study, the complete mitochondrial genome (mitogenome) of Clostera anachoreta (Lepidoptera: Notodontidae) was sequenced. It comprises 15,456 base pairs (bp), including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNA), 22 transfer RNAs (tRNA) and one non-coding control region (CR), as found in other lepidopterans. Gene order is identical to that of typical lepidopterans. There are 15 intergenic spacers ranging from 1 to 49bp, and 9 overlapping regions ranging from 1 to 8bp, occurring throughout the genome...
April 20, 2017: Genomics
https://www.readbyqxmd.com/read/28421039/population-structure-of-sclerotinia-subarctica-and-sclerotinia-sclerotiorum-in-england-scotland-and-norway
#3
John P Clarkson, Rachel J Warmington, Peter G Walley, Matthew Denton-Giles, Martin J Barbetti, Guro Brodal, Berit Nordskog
Sclerotinia species are important fungal pathogens of a wide range of crops and wild host plants. While the biology and population structure of Sclerotinia sclerotiorum has been well-studied, little information is available for the related species S. subarctica. In this study, Sclerotinia isolates were collected from different crop plants and the wild host Ranuculus ficaria (meadow buttercup) in England, Scotland, and Norway to determine the incidence of Sclerotinia subarctica and examine the population structure of this pathogen for the first time...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28402789/rust-fungi-on-panicum
#4
Jill E Demers, Miao Liu, Sarah Hambleton, Lisa A Castlebury
Rusts are economically important diseases of switchgrass (Panicum virgatum) and other Paniceae grasses. Phylogenetic analyses based on sequences of the nuc rDNA 5.8S internal transcribed spacer 2 region (ITS2), partial 28S region, and intergenic spacer region (IGS) of nuc rDNA showed that species of rust fungi infecting switchgrass are closely related within Puccinia. Variation among rbcLa sequences for the associated hosts sampled concurred with the original identifications. Five species infecting switchgrass were recognized: Puccinia graminicola (≡ Uromyces graminicola), P...
2017: Mycologia
https://www.readbyqxmd.com/read/28381961/investigation-of-genetic-diversity-of-fusarium-oxysporum-f-sp-fragariae-using-pcr-rflp
#5
Ji-Su Kim, Nam Jun Kang, Youn-Sig Kwak, Choungkeun Lee
Fusarium wilts of strawberry, caused by Fusarium oxysporum f. sp. fragariae, is a serious soil-borne disease. Fusarium wilt causes dramatic yield losses in commercial strawberry production and it is a very stubborn disease to control. Reliable chemical control of strawberry Fusarium wilt disease is not yet available. Moreover, other well-known F. oxysporum have different genetic information from F. oxysporum f. sp. fragariae. This analysis investigates the genetic diversity of strawberry Fusairum wilt pathogen...
April 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28372899/phylogenetically-diverse-group-of-native-bacterial-symbionts-isolated-from-root-nodules-of-groundnut-arachis-hypogaea-l-in-south-africa
#6
Sanjay K Jaiswal, Levini A Msimbira, Felix D Dakora
Groundnut is an economically important N​2-fixing legume that can contribute about 100-190kgNha(-1) to cropping systems. In this study, groundnut-nodulating native rhizobia in South African soils were isolated from root nodules. Genetic analysis of isolates was done using restriction fragment length polymorphism (RFLP)-PCR of the intergenic spacer (IGS) region of 16S-23S rDNA. A total of 26 IGS types were detected with band sizes ranging from 471 to 1415bp. The rhizobial isolates were grouped into five main clusters with Jaccard's similarity coefficient of 0...
March 7, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28362313/identification-and-characterization-of-spontaneous-auxotrophic-mutants-in-fusarium-langsethiae
#7
Olga Gavrilova, Anna Skritnika, Tatiana Gagkaeva
Analysis of 49 strains of Fusarium langsethiae originating from northern Europe (Russia, Finland, Sweden, UK, Norway, and Latvia) revealed the presence of spontaneous auxotrophic mutants that reflect natural intraspecific diversity. Our investigations detected that 49.0% of F. langsethiae strains were auxotrophic mutants for biotin, and 8.2% of the strains required thiamine as a growth factor. They failed to grow on vitamin-free media. For both prototrophic and auxotrophic strains, no growth defect was observed in rich organic media...
March 31, 2017: Microorganisms
https://www.readbyqxmd.com/read/28360398/nucleotide-diversity-and-phylogenetic-relationships-among-gladiolus-cultivars-and-related-taxa-of-family-iridaceae
#8
Niraj Singh, Baleshwar Meena, Ashish Kumar Pal, Roop Kumar Roy, Sri Krishna Tewari, Sushma Tamta, Tikam Singh Rana
The plastid genome regions of two intergenic spacers, psbA-trnH and trnL-trnF, were sequenced to study the nucleotide diversity and phylogenetic relationships among Gladiolus cultivars. Nucleotide diversity of psbA-trnH region was higher than trnL-trnF region of chloroplast. We employed Bayesian, maximum parsimony (MP) and neighbour-joining (NJ) approaches for phylogenetic analysis of Gladiolus and related taxa using combined datasets from chloroplast genome. The psbA-trnH and trnL-trnF intergenic spacers of Gladiolus and related taxa-like Babiana, Chasmanthe, Crocus, Iris, Moraea, Sisyrinchium, Sparaxis and two out group species (Hymenocallis littoralis and Asphodeline lutea) were used in the present investigation...
March 2017: Journal of Genetics
https://www.readbyqxmd.com/read/28345224/involvement-of-multiple-chlamydia-suis-genotypes-in-porcine-conjunctivitis
#9
R Chahota, H Ogawa, K Ohya, T Yamaguchi, K D E Everett, H Fukushi
Chlamydia suis has been detected in numerous disease conditions of pigs, particularly in eye infections. This study examined recurring conjunctivitis cases in five commercial pig farms in Japan. 40.5% of the cases were identified as Chlamydia positive using impression cytology of ocular smears and a genus-specific direct fluorescent antibody. C. suis was detected in 59.5% of the samples using PCR tests targeting 16S-23S rRNA intergenic spacer region (ISR) and ompA gene. Genetic analysis of PCR amplicons revealed nine sequence variants of 16S-23S rRNA ISR and 20 sequence variants within ompA gene...
March 27, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28338961/expressed-structurally-stable-inverted-duplicates-in-mammalian-genomes-as-functional-noncoding-elements
#10
Zhen-Xia Chen, Brian Oliver, Yong E Zhang, Ge Gao, Manyuan Long
Inverted duplicates are a type of repetitive DNA motifs consist of two copies of reverse complementary sequences separated by a spacer sequence. They can lead to genome instability and many may have no function, but some functional small RNAs are processed from hairpins transcribed from these elements. It is not clear whether the pervasive numbers of such elements in genomes, especially those of mammals, is the result of high generation rates of neutral or slightly deleterious duplication events or positive selection for functionality...
March 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28324231/occurrence-and-virulence-properties-of-vibrio-and-salinivibrio-isolates-from-tropical-lagoons-of-the-southern-caribbean-sea
#11
Milagro Fernández-Delgado, Paula Suárez, Sandra Giner, Virginia Sanz, Jessy Peña, Damarys Sánchez, M Alexandra García-Amado
The Vibrionaceae are Gram-negative bacteria present in marine and estuarine environments worldwide, including several species known as important pathogens to humans and aquatic organisms. The aim of this research was to investigate the occurrence and virulence properties of Vibrio and Salinivibrio isolated from lagoons at Cuare Wildlife Refuge and Margarita Island in the southern Caribbean Sea. Water, plankton and oyster samples were collected during October 2011 and March 2012 and examined by specific PCR and culture methods...
March 21, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28262480/presence-of-borrelia-in-different-populations-of-ixodes-pararicinus-from-northwestern-argentina
#12
Maria N Saracho Bottero, Patrick S Sebastian, Luis A Carvalho, Leonor Guardia Claps, Mariano Mastropaolo, Atilio J Mangold, José M Venzal, Santiago Nava
This work was performed to evaluate the presence of Borrelia in different populations of Ixodes pararicinus from northwestern Argentina (Jujuy, Salta and Tucumán provinces). Questing adults and nymphs of I. pararicinus were collected from vegetation, and I. pararicinus nymphs were also collected on birds. Eighty-two ticks were tested for Borrelia presence by PCR targeting the gene flagellin and the rrfA-rrlB intergenic spacer region. Pools of ticks positive to Borrelia were formed by two nymphs collected on Turdus rufiventris in Tucumán, one nymph collected on Syndactyla rufosuperciliata in Jujuy, one nymph collected on Turdus nigriceps in Tucumán, three nymphs collected on T...
February 27, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28187538/first-record-of-the-root-knot-nematode-i-meloidogyne-i-i-minor-i-in-new-zealand-with-description-sequencing-information-and-key-to-known-species-of-i-meloidogyne-i-in-new-zealand
#13
Zeng Qi Zhao, Wellcome Ho, Ruth Griffin, Michael Surrey, Robert Taylor, Lee T Aalders, Nigel L Bell, Yu Mei Xu, Brett J R Alexander
Meloidogyne minor Karssen et al. 2004 was collected from perennial ryegrass (Lolium perenne L.) growing in a sports ground in Christchurch, New Zealand. This is a new record for M. minor, the first report of this nematode occurring in New Zealand, and the second report from the southern hemisphere (after Chile). In general, the New Zealand isolate of M. minor corresponds well to the descriptions of M. minor given by Karssen et al. (2004). The New Zealand isolate is characterized by having a female with dorsally curved stylet, 13-14 μm long, with transversely ovoid knobs slightly sloping backwards from shaft; rounded perineal pattern; and male with stylet 16-19 μm long, large transversely ovoid knobs sloping slightly backwards from shaft; head region not set off, labial disc elevated, lateral lips prominent; and second stage juvenile 370-390 μm long, with hemizonid posterior but adjacent to excretory pore; tail 53-63 μm long; and a distinct hyaline tail terminus 14-18 μm long...
February 9, 2017: Zootaxa
https://www.readbyqxmd.com/read/28165925/molecular-detection-of-candidatus-bartonella-mayotimonensis-in-north-american-bats
#14
Thomas M Lilley, Cali A Wilson, Riley F Bernard, Emma V Willcox, Eero J Vesterinen, Quinn M R Webber, Laura Kurpiers, Jenni M Prokkola, Imran Ejotre, Allen Kurta, Kenneth A Field, DeeAnn M Reeder, Arto T Pulliainen
Candidatus Bartonella mayotimonensis was detected in 2010 from an aortic valve sample of a patient with endocarditis from Iowa, the United States of America. The environmental source of the potentially new endocarditis-causing Bartonella remained elusive. We set out to study the prevalence and diversity of bat-associated Bartonella in North America. During 2015, mist nets and harp traps were used to capture 92 bats belonging to two species: little brown myotis (Myotis lucifugus Le Conte 1831, n = 73) and the gray myotis (M...
April 2017: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/28155284/molecular-surveillance-of-spotted-fever-group-rickettsioses-in-wildlife-and-detection-of-i-rickettsia-sibirica-i-in-a-topi-i-damaliscus-lunatus-i-ssp-i-jimela-i-in-kenya
#15
David Ndeereh, Andrew Thaiyah, Gerald Muchemi, Antoinette A Miyunga
Spotted fever group rickettsioses are a group of tick-borne zoonotic diseases caused by intracellular bacteria of the genus Rickettsia. The diseases are widely reported amongst international travellers returning from most sub-Saharan Africa with fever, yet their importance in local populations largely remains unknown. Although this has started to change and recently there have been increasing reports of the diseases in livestock, ticks and humans in Kenya, they have not been investigated in wildlife. We examined the presence, prevalence and species of Rickettsia present in wildlife in two regions of Kenya with a unique human-wildlife-livestock interface...
January 30, 2017: Onderstepoort Journal of Veterinary Research
https://www.readbyqxmd.com/read/28154490/ribosomal-intergenic-spacer-1-based-characterization-of-button-mushroom-agaricus-bisporus-strains
#16
Hyuk Woo Kwon, Min Ah Choi, Dae Wook Kim, Youn-Lee Oh, Min Woo Hyun, Won-Sik Kong, Seong Hwan Kim
Breeding the button mushroom requires genetic information about its strains. This study was undertaken to genetically characterize four domestically bred button mushroom strains (Saea, Saejung, Saedo, Saeyeon cultivars) and to assess the possibility of using the intergenic spacer 1 (IGS1) region of rDNA as a genetically variable region in the genetic characterization. For the experiment, 34 strains of Agaricus bisporus, two strains of A. bitorquis, and one strain of A. silvaticus, from 17 countries were used...
December 2016: Mycobiology
https://www.readbyqxmd.com/read/28130406/prevalence-of-bartonella-species-infections-in-cats-in-southern-germany
#17
M Bergmann, T Englert, B Stuetzer, J R Hawley, M R Lappin, K Hartmann
Bartonella species are zoonotic pathogens, and infections in cats are common. However, prevalence in cats in Southern Germany is still unknown. Therefore, prevalence of Bartonella species DNA in blood of 479 Southern German cats was determined using a previously published conventional PCR targeting a fragment of the 16S-23S rRNA intergenic spacer region. Associations between Bartonella bacteraemia, housing conditions, feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) status, including progressive, regressive and abortive FeLV infection, were evaluated using Fisher's exact test...
April 1, 2017: Veterinary Record
https://www.readbyqxmd.com/read/28126698/identification-of-arcanobacterium-hippocoleae-by-maldi-tof-ms-analysis-and-by-various-genotypical-properties
#18
J-P Wickhorst, O Sammra, A A Hassan, M Alssashen, C Lämmler, E Prenger-Berninghoff, M Erhard, M Metzner, K Paschertz, M Timke, A Abdulmawjood
In the present study an Arcanobacterium hippocoleae strain isolated from a uterus swab of an apparently healthy mare could be identified by phenotypic properties, by MALDI-TOF MS analysis and genotypically by investigating the molecular targets 16S rDNA, 16S-23S rDNA intergenic spacer region and the genes encoding the β subunit of bacterial RNA polymerase (rpoB), elongation factor tu (tuf) and glyceraldehyde 3-phosphate dehydrogenase (gap). The presented data are one of the few reports about the species A...
January 17, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28114894/evolutional-dynamics-of-45s-and-5s-ribosomal-dna-in-ancient-allohexaploid-atropa-belladonna
#19
Roman A Volkov, Irina I Panchuk, Nikolai V Borisjuk, Marta Hosiawa-Baranska, Jolanta Maluszynska, Vera Hemleben
BACKGROUND: Polyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes. Here, we applied a combination of karyological and molecular methods to investigate chromosomal structure, molecular organization and evolution of ribosomal DNA (rDNA) in nightshade, Atropa belladonna (fam. Solanaceae), one of the oldest known allohexaploids among flowering plants. Because of their abundance and specific molecular organization (evolutionarily conserved coding regions linked to variable intergenic spacers, IGS), 45S and 5S rDNA are widely used in plant taxonomic and evolutionary studies...
January 23, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28111712/morphological-characterization-and-hsp70-igs-based-phylogenetic-analysis-of-two-microsporidian-parasites-isolated-from-antheraea-pernyi
#20
Yong Wang, Yutao Ru, Wei Liu, Deyi Wang, Jinglin Zhou, Yiren Jiang, Shenglin Shi, Li Qin
Two microsporidian isolates were extracted from single infected egg-laying tussah silk moth (Antheraea pernyi) in Liaoning Province, China. The microsporidia were subsequently grown in silk moth larvae, isolated, and subjected to morphological characterization (by light and transmission electron microscopy) and phylogenetic analysis (based on conserved genes). One type of spore was long-axis-oval in shape, measuring 4.71 × 1.95 μm, and the other type was short-axis-oval, measuring 3.64 × 2.17 μm. These dimensions were markedly different from those reported in the spores of the common microsporidia infecting A...
January 22, 2017: Parasitology Research
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