scholarly journals Differentiation of a Fusicoccum sp. Causing Panicle and Shoot Blight on California Pistachio Trees from Botryosphaeria dothidea

Plant Disease ◽  
2001 ◽  
Vol 85 (12) ◽  
pp. 1235-1240 ◽  
Author(s):  
Denise R. Smith ◽  
Themis J. Michailides ◽  
Glen R. Stanosz
Keyword(s):  
Internal Transcribed Spacer ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Its Region ◽  
Parsimony Analysis ◽  
Botryosphaeria Dothidea ◽  
Nuclear Rdna ◽  
Shoot Blight ◽  
Blight Disease ◽  
Pistachio Trees

A panicle and shoot blight disease of pistachio trees in California is caused by a fungus previously identified as the anamorph of Botryosphaeria dothidea. We have compared random amplified polymorphic DNA (RAPD) markers, nuclear rDNA internal transcribed spacer (ITS) region sequences, and conidium morphology of 15 isolates of the pistachio Fusicoccum to those of well-characterized isolates of B. dothidea, B. ribis, and F. luteum. Cluster analysis of RAPD markers separated the pistachio Fusicoccum isolates from B. dothidea, as did parsimony analysis of the ITS region sequences. Conidium size and shape were similar to those of B. ribis (Fusicoccum sp.) and F. luteum, but distinguishable from those of F. aesculi (the anamorph of B. dothidea). We conclude that the fungus causing panicle and shoot blight of pistachio is distinguishable from B. dothidea and is part of a complex containing B. ribis, F. luteum, and other fungi with Fusicoccum anamorphs.

scholarly journals Development of PCR Assays for the Identification of Species and Pathotypes of Elsinoë Causing Scab on Citrus

Plant Disease ◽  
2007 ◽  
Vol 91 (7) ◽  
pp. 865-870 ◽  
Author(s):  
J. W. Hyun ◽  
N. A. Peres ◽  
S.-Y. Yi ◽  
L. W. Timmer ◽  
K. S. Kim ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Sweet Orange ◽  
Random Amplified Polymorphic Dna ◽  
Its Region ◽  
The United States ◽  
Specific Primer ◽  
Identification Of Species ◽  
Orange Fruit ◽  
Pcr Assays ◽  
Primer Sets

Two scab pathogens of citrus, Elsinoë fawcettii and E. australis, cause citrus scab and sweet orange scab, respectively, and pathotypes of each species have been described. The two species cannot be readily distinguished by morphological or cultural characteristics and can be distinguished only by host range and the sequence of the internal transcribed spacer (ITS) region. In this study, random amplified polymorphic DNA (RAPD) assays clearly distinguished E. fawcettii and E. australis, and the sweet orange and natsudaidai pathotypes within E. australis also could be differentiated. We developed specific primer sets, Efaw-1 for E. fawcettii; Eaut-1, Eaut-2, Eaut-3, and Eaut-4 for E. australis; and EaNat-1 and EaNat-2 for the natsudaidai pathotype within E. australis using RAPD products unique to each species or pathotype. Other primer sets, Efaw-2 and Eaut-5, which were specific for E. fawcettii and E. australis, respectively, were designed from previously determined ITS sequences. The Efaw-1 and Efaw-2 primer sets successfully identified E. fawcettii isolates from Korea, Australia, and the United States (Florida) and the Eaut-1 to Eaut-5 primer sets identified both the sweet orange pathotype isolates of E. australis from Argentina and the natsudaidai pathotype isolates from Korea. The EaNat-1 and EaNat-2 primer sets were specific for isolates of the natsudaidai pathotype. The Efaw-1 and Efaw-2 primer sets successfully detected E. fawcettii from lesions on diseased leaves and fruit from Korea and primer pairs Eaut-1, Eaut-2, Eaut-3, Eaut-4, and Eaut-5 detected E. australis from lesions on sweet orange fruit from Brazil.

Genotypic Characterization of Rhizopus Spp. Tempeh and Usar: Traditional Inoculum of Tempeh in Indonesia

2020 ◽  
Vol 14 (3) ◽  
pp. 3
Author(s):  
Tati Barus ◽  
Jason Wiranata Sanjaya ◽  
Anastasia Tatik Hartanti ◽  
Adi Yulandi ◽  
Vivitri Dewi Prasasty ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Internal Transcribed Spacer ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Its Sequence ◽  
Rhizopus Microsporus ◽  
Rhizopus Delemar

Abstract. Soybeans tempeh (tempeh) is processed by fermentation using Rhizopus spp. Tempeh is an important source of protein in Indonesia. The traditional inoculum in fermentation locally is known as Usar which is made from the leaves of Hibiscus tiliaceus. However, Rhizopus information from Usar is still limited. Therefore, this study aims to identify and investigate the genetic diversity of Rhizopus species from Usar and tempeh based on the Internal Transcribed Spacer (ITS) sequence and the Random Amplified Polymorphic DNA (RAPD) markers. Twenty-three Rhizopus strains were isolated from Usar and ten Rhizopus strains were isolated from tempeh. Based on ITS sequences, the isolates were similar to R Rhizopus microsporus (30 isolates) and Rhizopus delemar (3 isolates) with 98-99% similarity. The genetics of R. microsporus and R. delemar are varied and different from the genetics of R. microsporus from tempeh. The growth temperature of R. microsporus varies from 33 to 48°C and R. delemar can grow to a maximum at 33°C. The role of R. microsporus and R. delemar from Usar in determining the quality of tempeh is still limited. Therefore, it needs to be investigated further.

Phylogenetic Abnalysis of Malaysian Pineapples Cultivars Based on the DNA Sequence of the Internal Transcribed Spacer Region

2013 ◽  
Vol 62 (2) ◽  
Author(s):  
Topik Hidayat ◽  
K. Chandrika ◽  
A. Farah Izana ◽  
S. A. Azman ◽  
W. Alina
Keyword(s):  
Internal Transcribed Spacer ◽  
Genomic Dna ◽  
Its Region ◽  
Biochemical Properties ◽  
Phylogenetic Study ◽  
Evolutionary Relationships ◽  
Parsimony Analysis ◽  
Internal Transcribed Spacer Region ◽  
Phylogenetic Status ◽  
Genetic Pattern

The phylogenetic study was conducted to determine the phylogenetic status and evolutionary relationships among the nine commercial pineapple cultivars using sequences of the internal transcribed spacer (ITS) region. Genomic DNA was extracted, and the ITS region was amplified and sequenced. Parsimony analysis revealed that Malaysian cultivars could be classified into two major groups based on the ITS region. The first group comprised of the cultivars Sarawak Green Local, Gandul, and N36 whereas the second group consisted of the cultivars Josapine, Yankee, Morris Bentanggur, Morris Gajah, MD2 and MD2/T. Several combinations of synapomorphic characters (leaf and fruit) support this classification system, suggesting the ITS region has the ability to determine the phylogenetic status and relationships of pineapple cultivars. Since each group has its own similar genetic pattern and presumably certain specific biochemical properties, the relationships of pineapple cultivars revealed in the phylogenetic tree can be used as a basis for successful hybridizations to generate new pineapple cultivars.

scholarly journals Genetic diversity of Rhizopus microsporus from traditional inoculum of tempeh in Indonesia based on ITS sequences and RAPD marker

2019 ◽  
Vol 20 (3) ◽  
pp. 847-852
Author(s):  
TATI BARUS ◽  
RONALDO HALIM ◽  
ANASTASIA TATIK HARTANTI ◽  
PAULUS KEVIN SAPUTRA
Keyword(s):  
Genetic Diversity ◽  
Internal Transcribed Spacer ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Its Sequences ◽  
Its Sequence ◽  
Rhizopus Microsporus ◽  
Universal Primer ◽  
Cluster 2

Abstract. Barus T, Halim R, Hartanti AT, Saputra PK. 2019. Genetic diversity of Rhizopus microsporus from traditional inoculum of tempeh in Indonesia based on ITS sequences and RAPD marker. Biodiversitas 20: 847-852. The main microorganism for tempeh fermentation is Rhizopus microsporus. These days, many tempeh producers use commercial inoculum, such as ‘Raprima’ as resource of R. microsporus. As a result, the genetic diversity of R. microsporus that had been reported in Indonesia has diminished. Information about genetic diversity is needed as a basis to select R. microsporus as tempeh inoculum. This research aims to investigate the genetic diversity of R. microsporus from waru leaves based on Internal Transcribed Spacer (ITS) Sequence and Random Amplified Polymorphic DNA (RAPD) markers. A total of 25 R. microsporus were isolated from traditional inoculum waru leaves (Inoculum 1) and traditional inoculum other than waru leaves (Inoculum 2). Amplification of ITS sequence was done using universal primer pairs of ITS-4 and ITS-5. Amplification of RAPD markers was done using primers OPC-08, OPC-19, OPQ-6, R-108, OPA-09 and OPJ-20. ITS sequence was not sufficient to compare the similarities among R. microsporus. On the other hand, RAPD markers successfully compared the similarities among 25 R. microsporus. A total of 25 R. microsporus were divided into 9 clusters. R. microsporus from Inoculum 1 grouped into Cluster 1, Cluster 3 and Cluster 4-8. Inoculum 2 grouped into Cluster 2 and Cluster 9. R. microsporus from tempeh grouped into Cluster 4 and was different from Inoculum 1 and Inoculum 2, except for TB3.

scholarly journals Population Structure of Botryosphaeria dothidea from Pistachio and Other Hosts in California

2001 ◽  
Vol 91 (7) ◽  
pp. 665-672 ◽  
Author(s):  
Zhonghua Ma ◽  
Eric W. A. Boehm ◽  
Yong Luo ◽  
Themis J. Michailides
Keyword(s):  
Genetic Variation ◽  
Host Species ◽  
Random Amplified Polymorphic Dna ◽  
Central Valley ◽  
Sexual Stage ◽  
Rare Occurrence ◽  
Botryosphaeria Dothidea ◽  
Dissimilarity Data ◽  
Haplotypic Diversity ◽  
Shoot Blight

Genetic diversity was investigated among California populations of Botryosphaeria dothidea, causal agent of Botryosphaeria panicle and shoot blight of pistachio, with random amplified polymorphic DNA (RAPD) and microsatellite-primed polymerase chain reaction (MP-PCR). We surveyed 120 isolates, 112 of which originated from the California Central Valley and included pistachio isolates (n = 52) and isolates from other plant species (n = 60). Out-group isolates (n = 8) were obtained from pistachio in Greece. There was a strong correlation (r = 0.99; P < 0.0001) between the RAPD- and MP-PCR dissimilarity data sets. Little genetic variation (haplotypic diversity [Hs] < 0.002) was detected among B. dothidea isolates collected from central and southern California pistachio plantings. We observed relatively high diversity for isolates from a northern California pistachio orchard (Hs = 0.0146), where the disease was first diagnosed, and from the Chico U.S. Department of Agriculture Germ Plasm Repository (Hs = 0.0726), where the first pistachio trees were planted in California in 1929. Isolates obtained from other hosts, especially those associated with the rare occurrence of the sexual stage of this fungus, showed the highest levels of diversity (Hs = 0.1689). Thirty-eight pistachio isolates (73.1%) had DNA fingerprints identical to 28 pycnidiospore-derived isolates (56.0%) obtained from other host species. Greenhouse inoculations demonstrated that all isolates obtained from other hosts were capable of infecting pistachio and produced characteristic disease symptomology. Thus, California populations of B. dothidea from pistachio are, for the most part, genetically uniform, with the sexual stage rare to absent. However, the rare occurrence of the sexual stage of B. dothidea on other hosts, and more importantly, the capacity of these isolates to infect pistachio, indicate that other host species may serve as sources of inoculum and genetic variation.

scholarly journals Polymorphism in Random Amplified and Nuclear rDNA Sequences Assessed in Certain Apple (Malus × domestica Borkh.) Cultivars

2011 ◽  
Vol 39 (2) ◽  
pp. 264
Author(s):  
Milosz SMOLIK ◽  
Katarzyna MALINOWSKA ◽  
Beata SMOLIK ◽  
Krzysztof PACEWICZ
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Its Region ◽  
Mantel Test ◽  
Rrna Genes ◽  
P Value ◽  
Molecular Tools ◽  
Nuclear Rdna ◽  
Rdna Sequences ◽  
Genetic Profiles

Eigth apple (Malus × domestica Borkh.) cultivars: ‘Delikates’, ‘Cortland’, ‘James Grieve’, ‘Lired’, ‘Jonathan’, ‘Golden Delicious’, ‘Jonagold’ and ‘Idared’ were characterized by two different molecular tools. These included analysis of the distribution of RAPD markers and length variability of the SSU, 5.8S, LSU and ITS region of the nuclear rRNA genes assessed in PCR reactions with different combinations of ‘universal’ primers. RAPD analysis was performed with 17 out of 24 RAPD primers tested. Those amplified a total of 183 loci (872 amplicons) out of which 34 (18.5%) were monomorphic, 128 (69.5%) were polymorphic and 22 (12%) cultivar-specific. Cultivar-specific RAPD products were detected for each apple cultivar. Amplification of the rDNA sequences showed variability. Fifty-four amplicons were generated in the experiment including 14 monomorphic, 26 polymorphic, and 14 cultivar-specific products. Altogether 232 amplicons were generated, whose length ranged from 220 to 940 bp. The analysis of dendrograms constructed on the basis of the analysis of RAPD genetic profiles and profiles amplified on rDNA matrices showed their significant correlation (Mantel test: r(AB) = 0.430; p-value (Two-tailed) = 0.024), which proves that the used methods correctly presented variability within the examined cultivars, and the molecular markers identified in the study can be considered appropriate.

Schoenus (Cyperaceae) is not monophyletic based on ITS nrDNA sequence data

2016 ◽  
Vol 29 (5) ◽  
pp. 265 ◽  
Author(s):  
Paul M. Musili ◽  
Adele K. Gibbs ◽  
Karen L. Wilson ◽  
Jeremy J. Bruhl
Keyword(s):  
Bayesian Inference ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Bootstrap Support ◽  
Nuclear Rdna ◽  
Its Nrdna ◽  
Rdna Sequence Data ◽  
Strong Bootstrap Support ◽  
Lines Of Evidence

We used nuclear rDNA-sequence data from the internal transcribed spacer (ITS) region to test the monophyly of Schoenus by using maximum parsimony and Bayesian inference. Schoenus is not monophyletic, with strong bootstrap support for most branches and congruence across analyses. nrITS does not resolve terminal taxa fully and, therefore, needs to be used in combination with other lines of evidence to address questions of species limits.

scholarly journals Laboratory diagnoses of the isolates of chestnut blight disease fungus Cryphonectria parasitica (MURR. BARR)

2010 ◽  
pp. 45-52
Author(s):  
László Radócz ◽  
László Irinyi ◽  
Károly Egyed
Keyword(s):  
Phylogenetic Relationships ◽  
Fungal Pathogens ◽  
Its Region ◽  
Cryphonectria Parasitica ◽  
Evolutionary Distance ◽  
Its Sequences ◽  
Chestnut Blight ◽  
Parsimony Analysis ◽  
Blight Disease

Chryphonectria parasitica, the casual agent of chestnut blight, is one of the most important fungal pathogens of chestnut (Castanea spp.) in Europe and Hungary. In this study, we analyzed the ITS region of five Cryphonectria parasitica strains isolated from different location of Hungary. The differences among the Cryphonectria parasitica isolates were not insignificant because only two sites were considered as informative for the parsimony analysis. As the differences among geographically different isolates were insignificant, we mean that the evolutionary distance by ITS sequences within Hungarian Cryphonectria parasitica isolates is too small to get well based consequences for the phylogenetic relationships.

EVALUATION OF PTYCHOBOTHRIDEAN CESTODES USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS FROM FRESH WATER FISHES IN GODAVARI BASIN (M.S.) INDIA

2017 ◽  
Vol 23 (2) ◽  
Author(s):  
SUNITA BORDE ◽  
ASAWARI FARTADE ◽  
AMOL THOSAR ◽  
RAHUL KHAWAL
Keyword(s):  
Fresh Water ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Band Pattern ◽  
Genomic Variation ◽  
Polymorphic Band ◽  
Rapd Profile ◽  
Band Size ◽  
Pcr Product ◽  
The Common

Ptychobothridean genera like Senga and Circumoncobothrium are the common parasites of fresh water fishes. The genotypic study of these parasites was taken by RAPD. The RAPD profile of these two parasites were not similar to each other as depicted by the band pattern in picture. These results suggest the presence of inter-specific polymorphism among cestode parasites of two different genera for RAPD analysis. The present study demonstrated that genetic differentiation of cestode parasites could be accomplished on the basis of genomic variation with polymorphic band pattern using RAPD. All the detected bands (PCR product) were polymorphic and band size ranged from 500-5000 bp in length. The RAPD of profiles using GBO-31, GBO-32, GBO-33, GBO-34, GBO-35 and GBO-36. Primers were able to characterize inter-specific polymorphism among the two genus ( Senga and Circumoncobothrium ). Genetic analysis suggests that Senga and Circumoncobothrium show genetic diversity with respect to RAPD patterns using all the six primers used for the present study. The genetic distance between the analyzed genuses ranged from 0.14 to 0.80. The differentiation of the two parasites on the basis of genetic markers could greatly facilitate study on the biology of these parasites.

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