Characterization of Fusarium spp. isolates by PCR-RFLP analysis of the intergenic spacer region of the rRNA gene (rDNA)

Alternaria isolates were obtained from various pistachio tissues collected in five orchards in California. For all isolates, morphological characteristics of the colony and sporulation apparatus were determined and compared with those of representative isolates of A. alternata, A. tenuissima, A. arborescens, and A. infectoria. A selection of the pistachio isolates and the representative Alternaria isolates were evaluated for pathogenicity to pistachio. Molecular characteristics of these isolates were determined using random amplified polymorphism DNA (RAPD) analysis, polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of nuclear intergenic spacer rDNA, and sequence analysis of nuclear internal transcribed spacer (ITS) rDNA. Based on morphological characteristics, the pistachio isolates were grouped as identical or very similar to either A. alternata, A. tenuissima, A. arborescens, or A. infectoria. Isolates from the alternata, tenuissima, and arborescens species-groups were pathogenic to pistachio and no significant differences in pathogenicity were observed. Isolates from the infectoria species-group were only weakly pathogenic to pistachio. Based on cluster analysis of RAPD and PCR-RFLP data, three distinct clusters were evident; the infectoria cluster, the arborescens cluster, and a combined alternata/tenuissima cluster. Based on analysis of ITS sequence data, the infectoria species-group was phylogenetically distinct from the other species-groups. Isolates of the alternata, tenuissima, and arborescens species-groups comprised a monophyletic clade in which the three species-groups could not be further resolved.

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Characterization of Sarcocystis species in domestic animals using a PCR-RFLP analysis of variation in the 18S rRNA gene: a cost-effective and simple technique for routine species identification

Experimental Parasitology ◽

10.1016/s0014-4894(03)00033-x ◽

2002 ◽

Vol 102 (3-4) ◽

pp. 212-217 ◽

Cited By ~ 33

Author(s):

Zhao-Qing Yang ◽

Qing-Qing Li ◽

Yang-Xian Zuo ◽

Xin-Wen Chen ◽

Yong-Jiu Chen ◽

...

Keyword(s):

Simple Technique ◽

Rflp Analysis ◽

Cost Effective ◽

Domestic Animals ◽

18S Rrna Gene ◽

Rrna Gene ◽

Sarcocystis Species ◽

Pcr Rflp ◽

Analysis Of Variation

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Isolation of Bartonella species from rodents in Taiwan including a strain closely related to ‘Bartonella rochalimae’ from Rattus norvegicus

Journal of Medical Microbiology ◽

10.1099/jmm.0.2008/004671-0 ◽

2008 ◽

Vol 57 (12) ◽

pp. 1496-1501 ◽

Cited By ~ 36

Author(s):

Jen-Wei Lin ◽

Chun-Yu Chen ◽

Wan-Ching Chen ◽

Bruno B. Chomel ◽

Chao-Chin Chang

Keyword(s):

Rattus Norvegicus ◽

Phylogenetic Analyses ◽

Intergenic Spacer ◽

Rflp Analysis ◽

23S Rrna ◽

Human Pathogens ◽

Bartonella Species ◽

Intergenic Spacer Region ◽

Pcr Rflp ◽

Rodent Populations

An increasing number of Bartonella species originally isolated from small mammals have been identified as emerging human pathogens. During an investigation of Bartonella infection in rodent populations carried out in Taiwan in 2006, a total of 58 rodents were tested. It was determined that 10.3 % (6/58) of the animals were Bartonella bacteraemic. After PCR/RFLP analysis, four isolates were identified as Bartonella elizabethae and one isolate as Bartonella tribocorum. However, there was one specific isolate with an unrecognized PCR/RFLP pattern. After further sequence and phylogenetic analyses of the gltA, ftsZ and rpoB genes, and the 16S–23S rRNA intergenic spacer region, the results indicated that this specific isolate from Rattus norvegicus was closely related to human pathogenic ‘Bartonella rochalimae’. Further studies need to be conducted to evaluate whether this rodent species could be a reservoir for ‘B. rochalimae’.

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Variability and characterization of mycotoxin-producing Fusarium spp isolates by PCR-RFLP analysis of the IGS-rDNA region

Antonie van Leeuwenhoek ◽

10.1007/s10482-005-9045-7 ◽

2006 ◽

Vol 89 (3-4) ◽

pp. 465-478 ◽

Cited By ~ 15

Author(s):

A. Llorens ◽

M. J. Hinojo ◽

R. Mateo ◽

A. Medina ◽

F. M. Valle-Algarra ◽

...

Keyword(s):

Rflp Analysis ◽

Fusarium Spp ◽

Pcr Rflp

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Identification of Armillaria species in Japan using PCR-RFLP analysis of rDNA intergenic spacer region and comparisons of Armillaria species in the world

Journal of Forest Research ◽

10.1007/s10310-004-0121-z ◽

2005 ◽

Vol 10 (3) ◽

pp. 173-179 ◽

Cited By ~ 7

Author(s):

Norihisa Matsushita ◽

Kazuo Suzuki

Keyword(s):

Intergenic Spacer ◽

Rflp Analysis ◽

Intergenic Spacer Region ◽

Pcr Rflp ◽

The World ◽

Rdna Intergenic Spacer ◽

Armillaria Species

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Detection and molecular characterization of phytoplasmas infecting apple trees in Poland

Horticultural Science ◽

10.17221/181/2013-hortsci ◽

2014 ◽

Vol 41 (No. 1) ◽

pp. 27-33 ◽

Cited By ~ 1

Author(s):

M. Cieślińska ◽

D.E. Kruczyńska

Keyword(s):

Rflp Analysis ◽

Rrna Gene ◽

Apple Trees ◽

Aster Yellows ◽

Candidatus Phytoplasma Mali ◽

Multiple Alignments ◽

Pcr Rflp ◽

Aster Yellows Phytoplasma ◽

Reference Strains

During 2010–2012, samples from 225 apple trees growing in six regions of Poland were tested for phytoplasmas. 16S rRNA gene and 16S-23S spacer region sequences were amplified from total DNAs prepared from phloem tissue of apple shoots. According to the results of PCR-RFLP and sequence analyses, apple trees were infected by Candidatus Phytoplasma mali and Ca. P. asteris. Fragments of 16S rDNA plus 16S-23S spacer region of the Ca. P. mali isolates digested with HpaII enzyme showed two restriction profiles: P-I and P-II. Multiple alignments of 16S rRNA gene fragments revealed that the isolates of Ca. P. mali shared 100% sequence identity among themselves as well as with reference strains AT and AP-15 of apple proliferation phytoplasma. The nucleotide sequence of the same region of <br /> Ca. P. asteris isolates confirmed the phylogenetic relationship with reference strains OAY (MIAY) and AY1 of aster yellows phytoplasma PCR-RFLP analysis of ribosomal protein (rpl22 and rpS3), secY, and tuf genes did not show the sequence diversity of the isolates of aster yellows phytoplasma.    

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Mycoplasma mucosicanis sp. nov., isolated from the mucosa of dogs

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.015750-0 ◽

2011 ◽

Vol 61 (4) ◽

pp. 716-721 ◽

Cited By ~ 12

Author(s):

Joachim Spergser ◽

Stefan Langer ◽

Simone Muck ◽

Kathrin Macher ◽

Michael Szostak ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Intergenic Spacer ◽

23S Rrna ◽

Rrna Gene ◽

Intergenic Spacer Region ◽

Pcr Rflp ◽

The 16S Rrna Gene ◽

Sequence Similarities

Fourteen Mycoplasma strains were isolated from the oral cavity and genital tract of asymptomatic dogs. Isolates had been preliminarily identified by conventional serological testing as Mycoplasma bovigenitalium, but in 16S–23S rRNA intergenic spacer PCR-RFLP assays the isolates exhibited an RFLP pattern distinct from M. bovigenitalium PG11T. Analysis of the 16S rRNA gene placed a representative of the isolates (strain 1642T) in the M. bovigenitalium subcluster of the Mycoplasma bovis cluster of mycoplasmas, with the highest sequence similarities to Mycoplasma californicum ST-6T (96.4 %), M. bovigenitalium PG11T (96.3 %) and Mycoplasma phocirhinis 852T (96.2 %). 16S rRNA gene sequence similarities almost equidistant from three recognized species and results obtained by sequence analysis of the 16S–23S rRNA intergenic spacer region, polar lipid profiles and serological reactions indicated that this organism represents a novel species of the genus Mycoplasma for which the name Mycoplasma mucosicanis sp. nov. is proposed, with strain 1642T ( = ATCC BAA-1895T = DSM 22457T) as the type strain.

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Genetic Characterization of Cryptosporidium cuniculus from Rabbits in Egypt

Pathogens ◽

10.3390/pathogens10060775 ◽

2021 ◽

Vol 10 (6) ◽

pp. 775

Author(s):

Doaa Naguib ◽

Dawn M. Roellig ◽

Nagah Arafat ◽

Lihua Xiao

Keyword(s):

Rflp Analysis ◽

Small Subunit ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Genetic Characteristics ◽

Glycoprotein Gene ◽

Cryptosporidium Spp ◽

Small Subunit Rrna Gene ◽

Pcr Rflp

Rabbits are increasingly farmed in Egypt for meat. They are, however, known reservoirs of infectious pathogens. Currently, no information is available on the genetic characteristics of Cryptosporidium spp. in rabbits in Egypt. To understand the prevalence and genetic identity of Cryptosporidium spp. in these animals, 235 fecal samples were collected from rabbits of different ages on nine farms in El-Dakahlia, El-Gharbia, and Damietta Provinces, Egypt during the period from July 2015 to April 2016. PCR-RFLP analysis of the small subunit rRNA gene was used to detect and genotype Cryptosporidium spp. The overall detection rate was 11.9% (28/235). All 28 samples were identified as Cryptosporidium cuniculus. The 16 samples successfully subtyped by the sequence analysis of the partial 60 kDa glycoprotein gene belonged to two subtypes, VbA19 (n = 1) and VbA33 (n = 15). As C. cuniculus is increasingly recognized as a cause of human cryptosporidiosis, Cryptosporidium spp. in rabbits from Egypt have zoonotic potential.

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