Molecular systematics of E-strain mycorrhizal fungi: Wilcoxina and its relationship to Tricharina (Pezizales)

1996 ◽  
Vol 74 (5) ◽  
pp. 773-779 ◽  
Author(s):  
Keith N. Egger
Keyword(s):  
Sequence Analysis ◽  
Mycorrhizal Fungi ◽  
Distinct Group ◽  
Interspecific Variation ◽  
Base Pairs ◽  
Internal Transcribed Spacer Region ◽  
Its1 Region ◽  
Rotting Wood ◽  
Interspecific Divergence ◽  
Wilcoxina Mikolae

Nuclear-encoded ribosomal RNA gene sequences (rDNA) spanning 107 base pairs at the 3′ end of the 18S gene, the 5′ internal transcribed spacer region (ITS1), and across divergent domain D1 near the 5′ end of the 28S gene were analyzed to infer a phylogeny for taxa of the E-strain mycorrhizal fungal genus Wilcoxina and to determine their relationship to representatives of the genus Tricharina. The phylogeny suggests that Wilcoxina and Tricharina, although related, should be maintained as separate genera. Wilcoxina taxa formed a distinct group that exhibited interspecific variation of 37.6% in the ITS1 region. Wilcoxina alaskana was the most distant taxon, which is consistent with its growth on an unusual substrate (rotting wood). It remains to be confirmed that this taxon is mycorrhizal. A cryptic Wilcoxina species, known only from root isolates, was found. Sequence analysis of the ITS1 region distinguished two varieties of Wilcoxina mikolae: var. mikolae and var. tetraspora. Among the taxa of Tricharina examined there was 31.2% variation in the ITS1 region. The most divergent taxon in the Tricharina group was Tricharina praecox, although sequence analysis was unable to distinguish the varieties described within this species. The remaining taxa in Tricharina formed a tight group with only 10.2% interspecific divergence in the ITS1 region. There is sequence evidence that at least two taxa are included in Tricharina gilva as presently delineated. As the sole report of mycorrhiza formation in Tricharina is shown to be based upon a misidentification, it therefore appears that only Wilcoxina taxa are mycorrhizal. Keywords: E-strain, Wilcoxina, Tricharina, mycorrhiza, ribosomal DNA, phylogeny.

scholarly journals DNA SEQUENCES OF FRAMESHIFT AND OTHER MUTATIONS INDUCED BY ICR-170 IN YEAST

Genetics ◽  
1985 ◽  
Vol 111 (2) ◽  
pp. 233-241
Author(s):  
Joachim F Ernst ◽  
D Michael Hampsey ◽  
Fred Sherman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Genetic Analysis ◽  
Dna Sequences ◽  
Induced Mutations ◽  
Sequence Analyses ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
Frameshift Mutations

ABSTRACT ICR-170-induced mutations in the CYC1 gene of the yeast Saccharomyces cerevisiae were investigated by genetic and DNA sequence analyses. Genetic analysis of 33 cyc1 mutations induced by ICR-170 and sequence analysis of eight representatives demonstrated that over one-third were frameshift mutations that occurred at one site corresponding to amino acid positions 29-30, whereas the remaining mutations were distributed more-or-less randomly, and a few of these were not frameshift mutations. The sequence results indicate that ICR-170 primarily induces G·C additions at sites containing monotonous runs of three G·C base pairs. However, some (see PDF) sites within the CYC1 gene were not mutated by ICR-170. Thus, ICR-170 is a relatively specific mutagen that preferentially acts on certain sites with monotonous runs of G·C base pairs.

Genetic Diversity and Origin of Siam Weed (Chromolaena odorata) in Australia

1998 ◽  
Vol 12 (1) ◽  
pp. 27-31 ◽  
Author(s):  
Leon J. Scott ◽  
Corinna L. Lange ◽  
Glenn C. Graham ◽  
David K. Yeates
Keyword(s):  
Genetic Diversity ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Southern Brazil ◽  
Chromolaena Odorata ◽  
Base Pairs ◽  
Its1 Sequence ◽  
Its1 Region ◽  
Native And Introduced Ranges ◽  
The U.S

Asynchronous flowering was noted in a recently discovered infestation of siam weed in north Queensland. This may indicate some genetic diversity in the infestation, increasing concerns about the origin of the infestation. Internal transcribed spacer 1 (ITS1) sequence data were obtained for siam weed individuals from north Queensland, Indonesia, Thailand, South Africa, Ivory Coast, Brazil, Colombia, and the U.S. The ITS1 region is 258 base pairs long, and the populations that flower at different times in north Queensland differ by four base substitutions. The genotype common in north Queensland is also reported throughout the native and introduced ranges. The other genotype is reported only in north Queensland and southern Brazil. These data, in conjunction with prior investigations into possible origins, indicate that Brazil is the most likely source of the infestation in Australia.

Ogataea kolombanensis sp. nov., Ogataea histrianica sp. nov. and Ogataea deakii sp. nov., three novel yeast species from plant sources

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3115-3123 ◽  
Author(s):  
Neža Čadež ◽  
Dénes Dlauchy ◽  
Peter Raspor ◽  
Gábor Péter
Keyword(s):  
Sequence Analysis ◽  
Olive Oil ◽  
Type Strain ◽  
Yeast Species ◽  
Novel Species ◽  
Large Subunit ◽  
Virgin Olive Oil ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
Lsu Rrna

Nine methanol-assimilating yeast strains isolated from olive oil sediments in Slovenia, extra virgin olive oil from Italy and rotten wood collected in Hungary were found to form three genetically separated groups, distinct from the currently recognized yeast species. Sequence analysis from genes of the small subunit (SSU) rRNA, internal transcribed spacer region/5.8S rRNA, large subunit (LSU) rRNA D1/D2 domains and translational elongation factor-1α (EF-1α) revealed that the three closely related groups represent three different undescribed yeast species. Sequence analysis of the LSU rRNA gene D1/D2 domains placed the novel species in the Ogataea clade. The three novel species are designated as Ogataea kolombanensis sp. nov. (type strain: ZIM 2322T = CBS 12778T = NRRL Y-63657T), Ogataea histrianica sp. nov. (type strain: ZIM 2463T = CBS 12779T = NRRL Y-63658T) and Ogataea deakii sp. nov. (type strain: NCAIM Y.01896T = CBS 12735T = NRRL Y-63656T).

scholarly journals Comparative Sequence Analysis of the tuf and recA Genes and Restriction Fragment Length Polymorphism of the Internal Transcribed Spacer Region Sequences Supply Additional Tools for Discriminating Bifidobacterium lactis from Bifidobacterium animalis

2003 ◽  
Vol 69 (12) ◽  
pp. 7517-7522 ◽  
Author(s):  
Marco Ventura ◽  
Ralf Zink
Keyword(s):  
Sequence Analysis ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Internal Transcribed Spacer Region ◽  
Bifidobacterium Lactis ◽  
Bifidobacterium Animalis ◽  
Restriction Fragment Length

ABSTRACT The relationship between Bifidobacterium lactis and Bifidobacterium animalis was examined by comparative analysis of tuf and recA gene sequences and by restriction fragment length polymorphism analysis of their internal 16S-23S transcribed spacer region sequences. The bifidobacterial strains investigated could be divided into two distinct groups within a single species based on the tuf, recA, and 16S-23S spacer region sequence analysis. Therefore, all strains of B. lactis and B. animalis could be unified as the species B. animalis and divided into two subspecies, Bifidobacterium animalis subsp. lactis and Bifidobacterium animalis subsp. animalis.

scholarly journals The ubiquitous potential Z-forming sequence of eucaryotes, (dT-dG)n . (dC-dA)n, is not detectable in the genomes of eubacteria, archaebacteria, or mitochondria.

1986 ◽  
Vol 6 (8) ◽  
pp. 3010-3013 ◽  
Author(s):  
D S Gross ◽  
W T Garrard
Keyword(s):  
Sequence Analysis ◽  
Nuclear Dna ◽  
Repeat Element ◽  
Phylogenetic Distribution ◽  
Base Pairs ◽  
Nuclear Genomes

The potential Z-forming sequence (dT-dG)n . (dC-dA)n is an abundant, interspersed repeat element that is ubiquitous in eucaryotic nuclear genomes. We report that in contrast to eucaryotic nuclear DNA, the genomes of eubacteria, archaebacteria, and mitochondria lack this sequence, since even a single tract of greater than or equal to 14 base pairs in length is not detectable through either hybridization or sequence analysis. Interestingly, the phylogenetic distribution of the (dT-dG)n . (dC-dA)n repeat exhibits a striking parallel to that of (dT-dC)n . (dG-dA)n, but not to other homocopolymeric sequences such as (dC-dG)n . (dC-dG)n or (dT-dA)n . (dT-dA)n.

scholarly journals Characterization of Metarhizium viride Mycosis in Veiled Chameleons (Chamaeleo calyptratus), Panther Chameleons (Furcifer pardalis), and Inland Bearded Dragons (Pogona vitticeps)

2016 ◽  
Vol 55 (3) ◽  
pp. 832-843 ◽  
Author(s):  
Volker Schmidt ◽  
Linus Klasen ◽  
Juliane Schneider ◽  
Jens Hübel ◽  
Michael Pees
Keyword(s):  
Sequence Analysis ◽  
Large Subunit ◽  
Antifungal Susceptibility ◽  
Clinical Signs ◽  
Antifungal Drugs ◽  
Lizard Species ◽  
Internal Transcribed Spacer Region ◽  
Content Type ◽  
Pogona Vitticeps ◽  
Chamaeleo Calyptratus

ABSTRACT Metarhizium viride has been associated with fatal systemic mycoses in chameleons, but subsequent data on mycoses caused by this fungus in reptiles are lacking. The aim of this investigation was therefore to obtain information on the presence of M. viride in reptiles kept as pets in captivity and its association with clinical signs and pathological findings as well as improvement of diagnostic procedures. Beside 18S ribosomal DNA (rDNA) (small subunit [SSU]) and internal transcribed spacer region 1 (ITS-1), a fragment of the large subunit (LSU) of 28S rDNA, including domain 1 (D1) and D2, was sequenced for the identification of the fungus and phylogenetic analysis. Cultural isolation and histopathological examinations as well as the pattern of antifungal drug resistance, determined by using agar diffusion testing, were additionally used for comparison of the isolates. In total, 20 isolates from eight inland bearded dragons ( Pogona vitticeps ), six veiled chameleons ( Chamaeleo calyptratus ), and six panther chameleons ( Furcifer pardalis ) were examined. Most of the lizards suffered from fungal glossitis, stomatitis, and pharyngitis or died due to visceral mycosis. Treatment with different antifungal drugs according to resistance patterns in all three different lizard species was unsuccessful. Sequence analysis resulted in four different genotypes of M. viride based on differences in the LSU fragment, whereas the SSU and ITS-1 were identical in all isolates. Sequence analysis of the SSU fragment revealed the first presentation of a valid large fragment of the SSU of M. viride . According to statistical analysis, genotypes did not correlate with differences in pathogenicity, antifungal susceptibility, or species specificity.

scholarly journals First Confirmed Report of Leaf Blight on Browntop Millet Caused by Bipolaris setariae in Southern Peninsular India

Plant Disease ◽  
2021 ◽  
Author(s):  
Ramesh Venkata Gutha ◽  
PALANNA K B ◽  
Boda Praveen ◽  
H. D. Vinaykumar ◽  
Prasanna S koti ◽  
...  
Keyword(s):  
The United States ◽  
Morphological Characters ◽  
Leaf Blight ◽  
Molecular Evidence ◽  
Post Inoculation ◽  
Conidial Suspension ◽  
Adaxial Side ◽  
Base Pairs ◽  
Internal Transcribed Spacer Region ◽  
Peninsular India

Browntop millet (Brachiaria ramosa (L.) Stapf), which is native to the United States, was recently introduced into India as one of the small millet crop. In September 2018, leaf blight symptoms were observed on cv. Dundu Korale on the adaxial side of the leaves in a field at Bangalore, India (13.0784oN, 77.5793oE). Initial lesions were brown with small yellow halo that ranged from 1 to 5 mm and eventually enlarged exhibiting light brown centers. Afterwards, spots coalesced and leaves were blighted. About 75% of the plants were infected in the field of 0.5 ha. Samples of symptomatic and asymptomatic leaves were collected, and nine isolates were recovered from culture on potato dextrose agar (PDA). Single conidial isolation was performed. Colonies were grey to olive green with regular margins at 7 days when cultured on PDA at 27 ± 1oC and 16 h light and 8 h dark cycles. Conidiophores were single or in clusters from 4.92 to 6.04 μm in width. Conidia were fusoid, cylindrical to slightly curved ranging from 38.50 to 130 μm in length and from 8.30 to 17 μm in width, with 4 to 10 distosepta (n =100). Hilum was flat to inconspicuous or slightly protruded. Based on the morphology, the pathogen was identified as a Bipolaris species according to the genus standard descriptions of Helminthosporium (Alcorn 1988). Misra and Prakash (1972) reported that Helminthosporium setariae causing leaf spot on browntop millet in India, but they did not provide any morphological or molecular evidence of identification. For molecular identification, the genomic DNA of isolate BTMH3 was extracted and the internal transcribed spacer region (ITS) and glyceraldehyde-3-phosphate dehydrogenase gene (GPD) were amplified using the pairs of primers ITS1/ITS4 (White et al. 1990) and GPD1/GPD2 (Berbee et al. 1999), respectively. BLAST analysis of ITS (MT750301; 562 matching base pairs) and GPD (MT896702; 562 matching base pairs) sequences showed 99.82% of identity with sequences of Bipolaris setariae (Sawada) Shoemaker type strain CBS 141.31 (ITS: EF452444 and GPD: EF513206). Pathogenicity was proved by spraying 10 healthy 20-day-old browntop millet plants with conidial suspension (106 conidia/ml). Control plants were sprayed with distilled water. Plants were covered with transparent polythene bags in a greenhouse at 28 ± 2oC and high relative humidity of 90%. Symptoms were observed at five days post inoculation. The pathogen was re-isolated from infected areas using the same protocol as before, whereas the control plants were symptomless. The re-isolated pathogen was confirmed as B. setariae based on morphological characters and PCR assay. To the best of our knowledge, this is the first report of leaf blight on browntop millet caused by B. setariae in the southern peninsular region of India. Disease specimen was deposited in Herbarium Cryptogamae Indiae Orientalis (HCIO), New Delhi, India with accession number 52209. Grain yield losses caused by leaf blight on browntop millet remain to be determined, however our findings indicate that cultivar cv. Dundu Korale is susceptible to B. setariae.

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