scholarly journals Occurrence and genetic variability of Candida parapsilosis sensu lato in Hungary

2007 ◽  
Vol 56 (2) ◽  
pp. 190-195 ◽  
Author(s):  
Sándor Kocsubé ◽  
Mónika Tóth ◽  
Csaba Vágvölgyi ◽  
Ilona Dóczi ◽  
Miklós Pesti ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Candida Parapsilosis ◽  
Sequence Data ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Its Region ◽  
Molecular Data ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Group I

The occurrence and genetic variability of Candida parapsilosis isolates in two Hungarian hospitals, located in Debrecen and Pécs, were examined. Among the 209 Candida isolates examined, 20 were found to belong to C. parapsilosis sensu lato, based on morphological, physiological and molecular data. The frequency of occurrence of C. parapsilosis isolates (9.6 %) was lower than that observed in Europe but higher than that observed previously in Hungary. The genetic variability of C. parapsilosis sensu lato isolates was also examined using random amplified polymorphic DNA (RAPD) analysis and sequence analysis of the intergenic transcribed spacer (ITS) region of the rRNA gene cluster. The genetic variability of the isolates was relatively high, as revealed by RAPD analysis. Two isolates were found to belong to the recently described Candida metapsilosis species (C. parapsilosis group III), based on ITS sequence data, RAPD analysis and phenotypic data. These two isolates could also be distinguished from C. parapsilosis sensu stricto isolates using a primer pair developed for the detection of C. parapsilosis group I isolates. To the best of the authors' knowledge, this is the first report on the identification of C. metapsilosis from bloodstream infection.

scholarly journals Genetic Diversity and Pathogenic Variability Among Isolates of Colletotrichum Species from Strawberry

2003 ◽  
Vol 93 (2) ◽  
pp. 219-228 ◽  
Author(s):  
Béatrice Denoyes-Rothan ◽  
Guy Guérin ◽  
Christophe Délye ◽  
Barbara Smith ◽  
Dror Minz ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Data ◽  
Its2 Sequence ◽  
Host Specialization ◽  
Pathogenicity Tests ◽  
Colletotrichum Spp ◽  
Rapd Polymorphism ◽  
Pathogenic Variability

Ninety-five isolates of Colletotrichum including 81 isolates of C. acutatum (62 from strawberry) and 14 isolates of C. gloeosporioides (13 from strawberry) were characterized by various molecular methods and pathogenicity tests. Results based on random amplified polymorphic DNA (RAPD) polymorphism and internal transcribed spacer (ITS) 2 sequence data provided clear genetic evidence of two subgroups in C. acutatum. The first subgroup, characterized as CA-clonal, included only isolates from strawberry and exhibited identical RAPD patterns and nearly identical ITS2 sequence analysis. A larger genetic group, CA-variable, included isolates from various hosts and exhibited variable RAPD patterns and divergent ITS2 sequence analysis. Within the C. acutatum population isolated from strawberry, the CA-clonal group is prevalent in Europe (54 isolates of 62). A subset of European C. acutatum isolates isolated from strawberry and representing the CA-clonal and CA-variable groups was assigned to two pathogenicity groups. No correlation could be drawn between genetic and pathogenicity groups. On the basis of molecular data, it is proposed that the CA-clonal subgroup contains closely related, highly virulent C. acutatum isolates that may have developed host specialization to strawberry. C. gloeosporioides isolates from Europe, which were rarely observed were either slightly or nonpathogenic on strawberry. The absence of correlation between genetic polymorphism and geographical origin in Colletotrichum spp. suggests a worldwide dissemination of isolates, probably through international plant exchanges.

Higher-level relationships among the eucalypts are resolved by ITS-sequence data

2002 ◽  
Vol 15 (1) ◽  
pp. 49 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Gay E. McKinnon ◽  
René E. Vaillancourt ◽  
Brad M. Potts
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
Phylogenetic Groups ◽  
Single Section ◽  
Western Australian ◽  
Genus Eucalyptus

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.

Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 201-210 ◽  
Author(s):  
F. N. Wachira ◽  
R. Waugh ◽  
W. Powell ◽  
C. A. Hackett
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Southeast Asia ◽  
Camellia Sinensis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Systematic Assessment ◽  
Tree Crop ◽  
Taxonomic Relationships

Camellia sinensis is a beverage tree crop native to Southeast Asia and introductions have been made into several nonindigenous countries. No systematic assessment of genetic variability in tea has been done anywhere. In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and taxonomic relationships in 38 clones belonging to the three tea varieties, assamica, sinensis, and assamica ssp. lasiocalyx. Extensive genetic variability was detected between species, which was partitioned into between and within population components. Seventy percent of the variation was detected within populations. Analyses based on band sharing separated the three populations in a manner consistent with both the present taxonomy of tea and with the known pedigrees of some clones. RAPD analysis also discriminated all of the 38 commercial clones, even those which cannot be distinguished on the basis of morphological and phenotypic traits.Key words: genetic diversity, RAPDs, Camellia sinensis.

scholarly journals Random amplified polymorphic DNA (RAPD) finger prints evidencing high genetic variability among marine angiosperms of India

2016 ◽  
Vol 97 (6) ◽  
pp. 1307-1315 ◽  
Author(s):  
Elangovan Dilipan ◽  
Jutta Papenbrock ◽  
Thirunavakkarasu Thangaradjou
Keyword(s):  
Genetic Variability ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Seagrass Species ◽  
Complex Species ◽  
Marine Angiosperms ◽  
Different Populations ◽  
High Degree ◽  
Identification Tool

In India 14 seagrass species can be found with monospecific genera (Enhalus, ThalassiaandSyringodium),Cymodoceawith two species andHalophilaandHalodulerepresented by more than two taxonomically complex species. Considering this, the present study was made to understand the level and pattern of genetic variability among these species collected from Tamilnadu coast, India. Random amplified polymorphic DNA (RAPD) analysis was used to evaluate the level of polymorphism existing between the species. Out of the 12 primers tested, 10 primers amplified 415 DNA fragments with an average of 41.5 fragments per primer. Of the total 415 amplified fragments only 123 (29.7%) were monomorphic and the remaining 292 (70.3%) were polymorphic for Indian seagrass species. Among the 10 primers used four are identified as the key primers capable of distinguishing all the Indian seagrasses with a high degree of polymorphism and bringing representative polymorphic alleles in all the tested seagrasses. From the present investigation, this study shows that the RAPD marker technique can be used not only as a tool to analyse genetic diversity but also to resolve the taxonomic uncertainties existing in the Indian seagrasses. The efficiency of these primers in bringing out the genetic polymorphism or homogeneity among different populations of theHalophilaandHalodulecomplex still has to be tested before recommending these primers as an identification tool for Indian seagrasses.

scholarly journals The use of random amplified polymorphic DNA to evaluate the genetic variability of Ponkan mandarin (Citrus reticulata Blanco) accessions

2000 ◽  
Vol 23 (1) ◽  
pp. 169-172 ◽  
Author(s):  
Helvécio Della Coletta Filho ◽  
Marcos Antonio Machado ◽  
M. Luiza P.N. Targon ◽  
Jorgino Pompeu Jr.
Keyword(s):  
Genetic Variability ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Point Mutations ◽  
The Other ◽  
Citrus Reticulata ◽  
Random Primers ◽  
Citrus Reticulata Blanco ◽  
Ponkan Mandarin

RAPD analysis of 19 Ponkan mandarin accessions was performed using 25 random primers. Of 112 amplification products selected, only 32 were polymorphic across five accessions. The absence of genetic variability among the other 14 accessions suggested that they were either clonal propagations with different local names, or that they had undetectable genetic variability, such as point mutations which cannot be detected by RAPD.

Phylogenetic position of Arabis arenicola and generic limits of Aphragmus and Eutrema (Brassicaceae) based on sequences of nuclear ribosomal DNA

2006 ◽  
Vol 84 (2) ◽  
pp. 269-281 ◽  
Author(s):  
Suzanne I. Warwick ◽  
Ihsan A. Al-Shehbaz ◽  
Connie A. Sauder
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
New Combinations ◽  
Arabidopsis Lyrata ◽  
Relationship Of

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 45 taxa were used to determine the phylogenetic relationship of Arabis arenicola to Arabis , Arabidopsis , Braya , and Eutrema , and that of Eutrema to the purportedly related genera Aphragmus , Lignariella , Neomartinella , Platycraspedum , Taphrospermum , and Thellungiella . Arabis arenicola was originally described as Eutrema in 1830, transferred to Arabis in 1898, and has remained in Arabis to the present, even though it is morphologically more similar to Arabidopsis, Braya, and Eutrema. Sequence data were obtained from representative taxa of Arabis, Arabidopsis, and related Boechera and Catolobus, Braya and Neotorularia, and Eutrema, Aphragmus, Lignariella, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. The five Arabis arenicola accessions examined had ITS sequences that were identical to each other and to four Arabidopsis lyrata accessions. In both maximum parsimony and maximum likelihood analyses, Arabis arenicola fell within the Arabidopsis clade and was closely aligned with Arabidopsis lyrata. Two of six purportedly related genera were not closely related to Eutrema. Both analyses placed Lignariella within a separate well-supported clade with Aphragmus, while the other four genera, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella, fell within a well-supported clade with Eutrema. Morphology and molecular data strongly suggest transferring Arabis arenicola to Arabidopsis, expanding Aphragmus to include Lignariella, and expanding Eutrema to include Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. New combinations in Arabidopsis and Aphragmus are proposed.

scholarly journals Nocardia neocaledoniensis sp. nov., a novel actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil

2004 ◽  
Vol 54 (2) ◽  
pp. 599-603 ◽  
Author(s):  
Danielle Saintpierre-Bonaccio ◽  
Luis A. Maldonado ◽  
Hamid Amir ◽  
René Pineau ◽  
Michael Goodfellow
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Sequence Data ◽  
Morphological Properties ◽  
Nocardia Asteroides ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Ultramafic Soil

The taxonomic position of an actinomycete isolated from a hypermagnesian ultramafic soil was examined using a polyphasic approach. The strain, designated SBHR OA6T, was shown to have chemical and morphological properties typical of members of the genus Nocardia. The organism was most closely associated with Nocardia asteroides using 16S rRNA gene sequence data. It showed a distinctive set of phenotypic properties that distinguished it from representatives of all species with validly published names classified in the genus Nocardia. The combined genotypic and phenotypic data show that strain SBHR OA6T (=DSM 44717T=NCIMB 13955T) merits description as the type strain of a novel Nocardia species, Nocardia neocaledoniensis sp. nov.

scholarly journals Characterization of Botrytis cinerea from Table Grapes in Chile Using RAPD-PCR

Plant Disease ◽  
1999 ◽  
Vol 83 (12) ◽  
pp. 1090-1094 ◽  
Author(s):  
J. R. Thompson ◽  
B. A. Latorre
Keyword(s):  
Botrytis Cinerea ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rhodotorula Glutinis ◽  
Test Sample ◽  
Vitis Vinifera L ◽  
Cryptococcus Laurentii ◽  
Similarity Coefficients ◽  
Table Grapes ◽  
Group I

Random amplified polymorphic DNA (RAPD) analysis was performed on 29 isolates of Botrytis cinerea Pers. ex Fr. isolated from table grapes (Vitis vinifera L.) and other crops in Chile with 29 decaprimers. No single primer was found to differentiate either the host or the geographical origin of each of the B. cinerea isolates tested. The DNA profiles obtained, particularly with primers OPA4 and OPA11, distinguished isolates of B. cinerea from other epiphyte fungi found on table grapes, including Alternaria alternata, Aspergillus niger, Cladosporium herbarum, Epiccocum nigrum, Rhizopus stolonifer, a Penicillium sp., and yeasts (Cryptococcus laurentii, Rhodotorula glutinis, and Saccharomyces cerevisiae). Regardless of host origin, primers OPA4 and OPA11 amplified a strong fragment of 1.2 kilobases (kb) and two fragments of 1.10 and 0.7 kb, respectively. These DNA fragments were obtained even when only one conidium of B. cinerea was in the test sample. Three main groups were clearly defined based on the genetic similarities found in additional RAPD analysis with 19 arbitrary decaprimers and 15 selected isolates of B. cinerea. The overall similarity coefficients (SC) between the groups obtained ranged from 0.326 to 0.891. Interestingly, all isolates from table grapes were included in group I (SC: 0.761 to 0.826), isolates from apple and tomato were in group II (SC: 0.739 to 0.848), while isolates from blueberry were either in group I (SC: 0.804) or III (SC: 0.673). Consequently, the genetic variability determined by RAPD analysis among these B. cinerea isolates suggested a possible host:pathogen relationship. However, further research is needed to clarify its pathological significance.

scholarly journals Micromonospora lupini sp. nov. and Micromonospora saelicesensis sp. nov., isolated from root nodules of Lupinus angustifolius

2007 ◽  
Vol 57 (12) ◽  
pp. 2799-2804 ◽  
Author(s):  
Martha E. Trujillo ◽  
Reiner M. Kroppenstedt ◽  
Carmen Fernández-Molinero ◽  
Peter Schumann ◽  
Eustoquio Martínez-Molina
Keyword(s):  
Type Strain ◽  
Sequence Data ◽  
Novel Species ◽  
Root Nodules ◽  
Taxonomic Status ◽  
Lupinus Angustifolius ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Fatty Acid Patterns

A study was conducted to determine the taxonomic status of six actinomycete strains isolated from root nodules of Lupinus angustifolius. The strains were filamentous, Gram-positive and produced single spores at the tip of the hyphae. Phylogenetic, chemotaxonomic and morphological analyses demonstrated that all six strains belonged to the genus Micromonospora. According to the 16S rRNA gene sequence data, the strains were divided into two clusters that are moderately related to Micromonospora mirobrigensis, Micromonospora matsumotoense and Micromonospora purpureochromogenes. Fatty acid patterns also supported the division of the strains, and significant differences between the two groups were found in the amounts of iso-15 : 0, iso-16 : 0, iso-16 : 1 and iso-17 : 0. Furthermore, the two groups showed physiological differences which included utilization of arabinose, trehalose, alanine and sucrose and xylan hydrolysis. Finally, DNA–DNA hybridization and ribotyping studies confirmed that each group represents a novel species. Based on the genotypic and phenotypic data, the novel species Micromonospora lupini sp. nov. (type strain Lupac 14NT =DSM 44874T =LMG 24055T) and Micromonospora saelicesensis sp. nov. (type strain Lupac 09T =DSM 44871T =LMG 24056T) are proposed.

scholarly journals Amycolatopsis plumensis sp. nov., a novel bioactive actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil

2005 ◽  
Vol 55 (5) ◽  
pp. 2057-2061 ◽  
Author(s):  
Danielle Saintpierre-Bonaccio ◽  
Hamid Amir ◽  
René Pineau ◽  
G. Y. Annie Tan ◽  
Michael Goodfellow
Keyword(s):  
Gene Sequence ◽  
Sequence Data ◽  
Novel Species ◽  
Morphological Properties ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Ultramafic Soil ◽  
Type Strains

The taxonomic position of an actinomycete isolated from a brown hypermagnesian ultramafic soil was examined using a polyphasic approach. The organism, which was designated SBHS Strp1T, was found to have chemical and morphological properties typical of Amycolatopsis strains. It was most closely associated with Amycolatopsis kentuckyensis, Amycolatopsis lexingtonensis, Amycolatopsis rifamycinica, Amycolatopsis pretoriensis and Amycolatopsis tolypomycina on the basis of 16S rRNA gene sequence data, and showed a unique pattern of phenotypic properties that distinguished it from the type strains of these taxa. The combined genotypic and phenotypic data show that the organism merits description as a novel species of Amycolatopsis. The name proposed for the novel species is Amycolatopsis plumensis sp. nov.; the type strain is SBHS Strp1T (=DSM 44776T=NRRL B-24324T).

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