Genetic variation in relation to substratum preferences of Hypogymnia physodes

2009 ◽  
Vol 41 (5) ◽  
pp. 547-555 ◽  
Author(s):  
Jan-Eric MATTSSON ◽  
Anne-Charlotte HANSSON ◽  
Louise LINDBLOM
Keyword(s):  
Dna Sequences ◽  
Sequence Variation ◽  
Its Region ◽  
Small Subunit ◽  
Hypogymnia Physodes ◽  
Gene Fragment ◽  
Statistical Parsimony ◽  
Total Dna ◽  
Study Sites ◽  
Group 1

AbstractGenetic variability and its relationship to substratum preferences within and among populations of the sorediate foliose lichen Hypogymnia physodes was investigated using sequence variation in the complete nrDNA internal transcribed spacer (ITS) region. A few samples of the putatively closely related, sorediate, H. tubulosa were also included. Samples were collected from each tree species in study sites in Estonia, Finland, and Sweden. In total, DNA sequences from 104 individuals of H. physodes and 16 of H. tubulosa were obtained. A group 1 intron situated at the end of the small subunit (SSU) of the nrDNA was detected in both species. Within-species variability was observed in both species: fifteen haplotypes were found for H. physodes and seven for H. tubulosa for the combined alignment of the intron and the ITS. Possible recombination within the total gene fragment was detected and hence the different regions (intron, ITS1, 5.8S, ITS2) were analysed separately. They show a different degree of variability both between each other and between the species. The number of haplotypes of H. physodes in the four regions are 5, 5, 1, and 5 and for H. tubulosa 5, 2, 1 and 2, respectively. A statistical parsimony estimation resulted in two unconnected networks; one containing all the samples of H. physodes and one containing all H. tubulosa samples. It was not possible to show different potentials of the different haplotypes for establishment on different substrata as the network of H. physodes indicates recombination within the ITS region which may be frequent enough to make this primarily clonally reproducing species to behave like a sexual species.

scholarly journals Molecular Identification and Hidden Diversity of Novel Daphnia Parasites from European Lakes

2009 ◽  
Vol 75 (22) ◽  
pp. 7051-7059 ◽  
Author(s):  
Justyna Wolinska ◽  
Sabine Giessler ◽  
Henrike Koerner
Keyword(s):  
Sequence Variation ◽  
Local Population ◽  
Its Region ◽  
Small Subunit ◽  
Diagnostic Tools ◽  
Rrna Gene ◽  
Natural Systems ◽  
Parasite Communities ◽  
Host Parasite ◽  
Sequence Similarities

ABSTRACT Parasites play important roles in local population dynamics and genetic structure. However, due to insufficient diagnostic tools, detailed host-parasite interactions may remain concealed by hidden parasite diversity in natural systems. Microscopic examination of 19 European lake Daphnia populations revealed the presence of three groups of parasites: fungi, microsporidia, and oomycetes. For most of these parasites no genetic markers have been described so far. Based on sequence similarities of the nuclear small-subunit and internal transcribed spacer (ITS) rRNA gene regions, one fungus, four microsporidian, and nine oomycete taxa were discovered in 147 infected Daphnia (and/or three other zooplankton crustaceans). Additionally, cloning of rRNA gene regions revealed parasite sequence variation within host individuals. This was most pronounced in the ITS region of one microsporidian taxon, where the within-host sequence variation ranged from 1.7% to 5.3% polymorphic sites for parasite isolates from 14 different geographical locations. Interestingly, the parasite isolates from close locations grouped together based on sequence similarities, suggesting that there was parasite dispersal. Taken together, the data obtained in this study revealed hidden diversity of parasite communities in Daphnia lake populations. Moreover, a higher level of resolution for identifying parasite strains makes it possible to test new hypotheses with respect to parasite dispersal, transmission routes, and coinfection.

scholarly journals Small genomic insertions form enhancers that misregulate oncogenes

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Brian J. Abraham ◽  
Denes Hnisz ◽  
Abraham S. Weintraub ◽  
Nicholas Kwiatkowski ◽  
Charles H. Li ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Tumour Cell ◽  
Sequence Variation ◽  
Coding Regions ◽  
Active Enhancer ◽  
Dna Sequence Variation ◽  
Total Dna ◽  
Coding Variants ◽  
Dna Alignment ◽  
Genomic Insertions

Abstract The non-coding regions of tumour cell genomes harbour a considerable fraction of total DNA sequence variation, but the functional contribution of these variants to tumorigenesis is ill-defined. Among these non-coding variants, somatic insertions are among the least well characterized due to challenges with interpreting short-read DNA sequences. Here, using a combination of Chip-seq to enrich enhancer DNA and a computational approach with multiple DNA alignment procedures, we identify enhancer-associated small insertion variants. Among the 102 tumour cell genomes we analyse, small insertions are frequently observed in enhancer DNA sequences near known oncogenes. Further study of one insertion, somatically acquired in primary leukaemia tumour genomes, reveals that it nucleates formation of an active enhancer that drives expression of the LMO2 oncogene. The approach described here to identify enhancer-associated small insertion variants provides a foundation for further study of these abnormalities across human cancers.

scholarly journals First Report of Dollar Spot of Sandbur Caused by Sclerotinia homoeocarpa in Oklahoma

Plant Disease ◽  
2014 ◽  
Vol 98 (8) ◽  
pp. 1160-1160
Author(s):  
F. Flores ◽  
N. R. Walker
Keyword(s):  
Warm Season ◽  
Its Region ◽  
Small Subunit ◽  
Type I ◽  
Academic Press ◽  
Sclerotinia Homoeocarpa ◽  
Dollar Spot ◽  
First Report ◽  
Small Subunit Rdna ◽  
Disturbed Soils

Sandbur (Cenchrus incertus Curtis) is a warm-season, annual, noxious, grassy weed native to southern North America. It is common in sandy, disturbed soils and can also be found in home lawns and sport fields where low turf density facilitates its establishment. In July 2013, after a period of frequent rainfall and heavy dew, symptoms of dollar spot-like lesions (1) were observed on sandbur plants growing in a mixed stand of turf-type and native warm-season grasses in Logan County, Oklahoma. Lesions, frequently associated with leaf sheaths, were tan and surrounded by a dark margin. Symptomatic leaves were surface sterilized and plated on potato dextrose agar amended with 10 ppm rifampicin, 250 ppm ampicillin, and 5 ppm fenpropathrin. After incubation, a fungus morphologically identical to Sclerotinia homoeocarpa Bennett was consistently isolated. The nuclear ribosomal internal transcribed spacer (ITS) region of two different isolates, SCL2 and SCL3, were amplified using primers ITS4 and ITS5 (2). The DNA products were sequenced and BLAST analyses were used to compare sequences with those in GenBank. The sequence for isolate SLC2 was 869 bp, contained a type I intron in the 18S small subunit rDNA, and was identical to accession EU123803. The ITS sequence for isolate SLC3 was 535 bp and identical to accession EU123802. Twenty-five-day-old seedlings of C. incertus were inoculated by placing 5-mm-diameter agar plugs, colonized by mycelia of each S. homoeocarpa isolate, onto two of the plants' leaves. Plugs were held in place with Parafilm. Two plants were inoculated with each isolate and sterile agar plugs were placed on two leaves of another seedling as control. Plants were incubated in a dew chamber at 20°C and a 12-h photoperiod. After 3 days of incubation, water-soaked lesions surrounded by a dark margin appeared on inoculated plants only. Fungi that were later identified as S. homoeocarpa isolates SLC2 and SLC3 by sequencing of the ITS region were re-isolated from symptomatic leaves, fulfilling Koch's postulates. To our knowledge, this is the first report of dollar spot on sandbur. References: (1) R. W. Smiley et al. Page 22 in: Compendium of Turfgrass Diseases. 3rd ed. The American Phytopathological Society, St. Paul, MN, 2005. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA, 1990.

Systematic status of Campydora Cobb, 1920 (Nematoda: Campydorina)

Nematology ◽  
2003 ◽  
Vol 5 (5) ◽  
pp. 699-711 ◽  
Author(s):  
Peter Mullin ◽  
Timothy Harris ◽  
Thomas Powers
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Systematic Position ◽  
Nominal Species ◽  
Competing Hypotheses ◽  
Small Subunit Ribosomal Dna

AbstractThe systematic position of Campydora Cobb, 1920, which possesses many unique morphological features, especially in pharyngeal structure and stomatal armature, has long been a matter of uncertainty with the 'position of the Campydorinae' (containing only Campydora) being questionable. A review of the morphology of C. demonstrans, the only nominal species of Campydora concluded that the species warranted placement as the sole member of a monotypic suborder, Campydorina, in the order Dorylaimida. Others placed Campydorina in the order Enoplida. We conducted phylogenetic analyses, using 18s small subunit ribosomal DNA sequences generated from a number of taxa in the subclasses Enoplia and Dorylaimia, to evaluate these competing hypotheses. Although precise taxonomic placement of the genus Campydora and the identity of its closest living relatives is in need of further investigation, our analyses, under maximum parsimony, distance, and maximum likelihood criteria, unambiguously indicate that Campydora shares a common, more recent, ancestry with genera such as Alaimus, Pontonema, Tripyla and Ironus (Enoplida), rather than with any members of Dorylaimida, Mononchida or Triplonchida.

Estrogen and progesterone receptor-binding sites on the chicken vitellogenin II gene: synergism of steroid hormone action

1988 ◽  
Vol 8 (12) ◽  
pp. 5323-5330
Author(s):  
A C Cato ◽  
E Heitlinger ◽  
H Ponta ◽  
L Klein-Hitpass ◽  
G U Ryffel ◽  
...  
Keyword(s):  
Progesterone Receptor ◽  
Receptor Binding ◽  
Dna Sequences ◽  
Binding Sites ◽  
Consensus Sequence ◽  
Chloramphenicol Acetyltransferase ◽  
Synergistic Action ◽  
Gene Fragment ◽  
T47d Cells ◽  
Vitellogenin Gene

The chicken vitellogenin II gene is transcriptionally activated by estrogens. In transient transfection experiments in human T47D cells that contain receptors for various steroids, we showed estradiol, progestin, and androgen responses of a chimeric chicken vitellogenin II construct. This construct consists of DNA sequences from -626 to -590 upstream of the start of transcription of the chicken vitellogenin gene linked to the herpes simplex virus thymidine kinase promoter driving the transcription of the bacterial chloramphenicol acetyltransferase gene. Treatment of the transfected T47D cells with a combination of estradiol and the progestin R5020 led to a superinduction of chloramphenicol acetyltransferase activity, showing a synergistic action of these two steroids. This synergism was not observed upon treatment of the transfected cells with estradiol and the androgen dihydrotestosterone. Using point mutations in the vitellogenin gene fragment, we showed in functional and in in vitro DNase I footprinting assays with a purified progesterone receptor that, for the synergistic action of estradiol and R5020 to occur, the progesterone receptor must be bound to the vitellogenin gene fragment. The progesterone receptor-binding site was localized at -610 to -590, close to the consensus sequence (-626 to -613) for estrogen receptor binding and function. We therefore demonstrate here that two different steroid hormones can be functionally synergistic through the interaction of their corresponding receptors with two different binding sites adjacent to one another.

Fungal composition of lichen thalli assessed by single strand conformation polymorphism

2010 ◽  
Vol 42 (4) ◽  
pp. 461-473 ◽  
Author(s):  
Lucia MUGGIA ◽  
Martin GRUBE
Keyword(s):  
Direct Sequencing ◽  
Its Region ◽  
Single Strand Conformation Polymorphism ◽  
Morphological Characters ◽  
Single Strand ◽  
Specific Primers ◽  
Lichenicolous Fungi ◽  
Large Numbers ◽  
Total Dna ◽  
Conformation Polymorphism

AbstractFungi that are unrelated to the mycobiont species frequently colonize lichens. Some of these fungal colonists are described lichenicolous fungi, lichen parasites and pathogens that produce recognizable morphological characters, while others apparently produce no noticeable structures. Here we apply the single strand conformation polymorphism (SSCP) technique to directly assess the abundance of different fungi in lichens. Twenty-eight lichen thalli were chosen, some with and some without externally visible symptoms of parasite infection, and these were subjected to total DNA extraction. PCR was conducted with fungal-specific primers for the ITS region of ribosomal DNA. Single strands of the products were separated on native acrylamide gels. The majority of lichen specimens, both infected and those without symptoms, displayed more than one band in the stained gels. In one case, 14 bands were detected using SSCP. Some of these bands apparently represent other neighbouring lichens in the habitat, but many are apparently non-lichen-forming. Since few lichen-associated fungi have been cultured and sequenced, it is difficult to know if SSCP bands represent obligate lichenicolous fungi, other asymptomatic lichen parasites, or fungi not obligately associated with lichens, but our results indicate that large numbers of non-lichen-forming fungi commonly co-occur with lichens in nature. For specimens of the filamentous lichens Cystocoleus ebeneus and Racodium rupestre we used cloned sequences to compare the number of sequences obtained by the SSCP method to the number obtained by direct sequencing of thallus extracts, and we generally found that more sequences could be detected by SSCP than could be seen by direct sequencing.

Towards a monophyletic classification of Lejeuneaceae III: the systematic position of Leiolejeunea

Phytotaxa ◽  
2014 ◽  
Vol 170 (3) ◽  
pp. 187 ◽  
Author(s):  
ALFONS SCHÄFER-VERWIMP ◽  
KATHRIN FELDBERG ◽  
SHANSHAN DONG ◽  
HUUB VAN MELICK ◽  
DENILSON F. PERALTA ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Its Region ◽  
Systematic Position ◽  
Leaf Cell ◽  
Oil Bodies ◽  
Sister Relationship ◽  
First Time

The derived liverwort Leiolejeunea grandiflora was recollected at the type locality in Jamaica after more than 100 years. The characteristics of its oil bodies were described for the first time based on the new collections. Each leaf cell possesses 2-4(-6) rather small, subhomogeneous to very finely segmented, subglobose to ellipsoidal, colorless oil bodies. The plants were either dioicous or autoicous. DNA sequences of two chloroplast regions (trnL-trnF, rbcL) and the nuclear ribosomal ITS region were obtained for two accessions of Leiolejeunea to enable the inference of the phylogenetic relationships of these plants. Based on Bayesian inference of phylogeny as well as maximum parsimony and maximum likelihood analyses of a dataset including 87 representatives of Lejeuneaceae, Leiolejeunea was found as the putative sister to either Echinolejeuneinae or Cheilolejeuneinae. Thus, we propose the new monogeneric subtribe Leiolejeuneinae with relationships to Cheilolejeuneinae and Echinolejeuneinae. The analyses included also one accession of the generitype of Cheilolejeunea, C. decidua [= Cheilolejeunea adnata]. This species was found in a well supported sister relationship with Cystolejeunea. To avoid nomenclatural confusion, we propose a wide genus concept for Cheilolejeunea including Aureolejeunea, Cyrtolejeunea, Cystolejeunea, Evansiolejeunea, Leucolejeunea, and Omphalanthus.

scholarly journals First Report of Anthracnose of Onion Caused by Colletotrichum coccodes in Ohio

Plant Disease ◽  
2014 ◽  
Vol 98 (9) ◽  
pp. 1271-1271 ◽  
Author(s):  
F. Baysal-Gurel ◽  
N. Subedi ◽  
D. P. Mamiro ◽  
S. A. Miller
Keyword(s):  
Leaf Tissue ◽  
Its Region ◽  
The United States ◽  
Tween 20 ◽  
Colletotrichum Coccodes ◽  
Academic Press ◽  
Conidial Suspension ◽  
First Report ◽  
Allium Cepa L ◽  
Total Dna

Dry bulb onion (Allium cepa L. cvs. Pulsar, Bradley, and Livingston) plants with symptoms of anthracnose were observed in three commercial fields totaling 76.5 ha in Huron Co., Ohio, in July 2013. Symptoms were oval leaf lesions and yellowing, curling, twisting, chlorosis, and death of leaves. Nearly half of the plants in a 32.8-ha field of the cv. Pulsar were symptomatic. Concentric rings of acervuli with salmon-colored conidial masses were observed in the lesions. Conidia were straight with tapered ends and 16 to 23 × 3 to 6 μm (2). Colletotrichum coccodes (Wallr.) S. Hughes was regularly isolated from infected plants (2). Culturing diseased leaf tissue on potato dextrose agar (PDA) amended with 30 ppm rifampicin and 100 ppm ampicillin at room temperature yielded white aerial mycelia and salmon-colored conidial masses in acervuli. Numerous spherical, black microsclerotia were produced on the surface of colonies after 10 to 14 days. To confirm pathogen identity, total DNA was extracted directly from a 7-day-old culture of isolate SAM30-13 grown on PDA, using the Wizard SV Genomic DNA Purification System (Promega, Madison, WI) following the manufacturer's instructions. The ribosomal DNA internal transcribed spacer (ITS) region was amplified by PCR using the primer pair ITS1 and ITS4 (2), and sequenced. The sequence, deposited in GenBank (KF894404), was 99% identical to that of a C. coccodes isolate from Michigan (JQ682644) (1). Ten onion seedlings cv. Ebenezer White at the two- to three-leaf stage of growth were spray-inoculated with a conidial suspension (1 × 105 conidia/ml containing 0.01% Tween 20, with 10 ml applied/plant). Plants were maintained in a greenhouse (21 to 23°C) until symptoms appeared. Control plants were sprayed with sterilized water containing 0.01% Tween 20, and maintained in the same environment. After 30 days, sunken, oval lesions each with a salmon-colored center developed on the inoculated plants, and microscopic examination revealed the same pathogen morphology as the original isolates. C. coccodes was re-isolated consistently from leaf lesions. All non-inoculated control plants remained disease-free, and C. coccodes was not re-isolated from leaves of control plants. C. coccodes was reported infecting onions in the United States for the first time in Michigan in 2012 (1). This is the first report of anthracnose of onion caused by C. coccodes in Ohio. Unusually wet, warm conditions in Ohio in 2013 likely contributed to the outbreak of this disease. Timely fungicide applications will be necessary to manage this disease in affected areas. References: (1) A. K. Lees and A. J. Hilton. Plant Pathol. 52:3. 2003. (2) L. M. Rodriguez-Salamanca et al. Plant Dis. 96:769. 2012. (3) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA, 1990.

scholarly journals Survey, Identification, and Characterization of Cylindrocarpon-Like Asexual Morphs in Spanish Forest Nurseries

Plant Disease ◽  
2018 ◽  
Vol 102 (11) ◽  
pp. 2083-2100 ◽  
Author(s):  
Beatriz Mora-Sala ◽  
Ana Cabral ◽  
Maela León ◽  
Carlos Agustí-Brisach ◽  
Josep Armengol ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Elongation Factor ◽  
Its Region ◽  
Phylogenetic Position ◽  
Translation Elongation ◽  
Forest Nurseries ◽  
Asexual Morphs ◽  
Identification And Characterization ◽  
Elongation Factor 1

Cylindrocarpon-like asexual morphs infect herbaceous and woody plants, mainly in agricultural scenarios, but also in forestry systems. The aim of the present study was to characterize a collection of Cylindrocarpon-like isolates recovered from the roots of a broad range of forest hosts from nurseries showing decline by morphological and molecular studies. Between 2009 and 2012, 17 forest nurseries in Spain were surveyed and a total of 103 Cylindrocarpon-like isolates were obtained. Isolates were identified based on DNA sequences of the partial gene regions histone H3 (his3). For the new species, the internal transcribed spacer and intervening 5.8S nrRNA gene (ITS) region, β-tubulin (tub2), and translation elongation factor 1-α (tef1) were also used to determine their phylogenetic position. Twelve species belonging to the genera Cylindrodendrum, Dactylonectria, and Ilyonectria were identified from damaged roots of 15 different host genera. The species C. alicantinum, D. macrodidyma, D. novozelandica, D. pauciseptata, D. pinicola, D. torresensis, I. capensis, I. cyclaminicola, I. liriodendri, I. pseudodestructans, I. robusta, and I. rufa were identified. In addition, two Dactylonectria species (D. hispanica sp. nov. and D. valentina sp. nov.), one Ilyonectria species (I. ilicicola sp. nov.), and one Neonectria species (N. quercicola sp. nov.) are newly described. The present study demonstrates the prevalence of this fungal group associated with seedlings of diverse hosts showing decline symptoms in forest nurseries in Spain.

Sign in / Sign up

Export Citation Format

Share Document