Molecular characterization of Paecilomyces fumosoroseus (Deuteromycotina: Hyphomycetes) isolates

ITS and RAPD analyses were used to investigate molecular variations within samples of Paecilomyces isolates and to resolve five morphologically atypical isolates resembling P. fumosorosus, obtained from whitefly in Northern Paraná State. The ITS4-ITS5 amplicon was 700 base pairs (bp) long in all isolates. The five isolates of Paecilomyces not assigned to species produced restriction profiles identical to all the reference strains of P. fumosoroseus. The extent of fingerprint variability observed by RAPD was sufficient to discriminate all the isolates. The genetic similarity among unidentified isolates and strains of P. fumosoroseus was even higher than that observed among reference strains of this species, allowing us to conclude that isolates CNPso-P77, CNPso-P78, CNPso-P80, CNPso-P85 and CNPso-P91 are P. fumosoroseus.

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Molecular Characterization of 12 Mango Germplasm Using RAPD markers

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v20i1.5972 ◽

2010 ◽

Vol 20 (1) ◽

pp. 91-99

Author(s):

R. C. Jena ◽

K. C. Samal ◽

P. K. Chand ◽

B. K. Das

Keyword(s):

Molecular Characterization ◽

Rapd Markers ◽

Mangifera Indica ◽

Pcr Amplification ◽

Similarity Coefficient ◽

Group Method ◽

Base Pairs ◽

Relationship Analysis ◽

Pair Group

Randomly amplified polymorphic DNA (RAPD) markers were used for the genetic variation and relationship analysis among 12 Mango (Mangifera indica L.) germplasm. Five oligonucleotide primers were employed to amplify DNA from 12 cultivars. PCR amplification with five primers generated 45 reproducible, clear and distinct bands, out of which 41 bands are considered polymorphic and the remaining four fragments (8.88%) monomorphic. The size of amplified product ranged from 200 (RPI-5) to 3000 base pairs (RPI-1) with an average of nine bands per primer. The average polymorphism in all the 12 cultivars using the five primers was found to be 91.91%. Among all the primers RPI-2 and RPI-4 have shown 100% polymorphism while RPI-5 was found to be least polymorphism (81.81%). One specific band, namely was found with RPI-5, in a particular variety, Chiratpuri. The UPGMA (Unweighted Pair Group Method of Arithmetic Mean) dendrogram based on Jaccard’s similarity coefficient segregated the 12 mango germplasm into two clusters. Langra, Chiratpuri, Pravasankar, Alphanso, Sindhu and Kesar formed one cluster and rest six mango germplasm grouped together into another cluster. Sindhu and Alphanso cultivar pair was very close to each other with highest similarity coefficient (0.78), which was comparatively higher than all other cultivar pairs. On the other hand, Pravasankar and Neelam cultivar pair was more distinct to each other with the lowest intervarietal similarity coefficient 0.38. This study showed clearly that cultivars from Orissa unveiled maximum diversity and indicated the potential of RAPD markers for the identification of management of mango germplasm for breeding purposes. Key words: Molecular characterization, Mango germplasm, Dversity D.O.I. 10.3329/ptcb.v20i1.5972 Plant Tissue Cult. & Biotech. 20(1): 91-99, 2010 (June)

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Molecular characterization of stolbur phytoplasmas in pepper and tomato from Bulgaria

BIO Web of Conferences ◽

10.1051/bioconf/20201800025 ◽

2020 ◽

Vol 18 ◽

pp. 00025

Author(s):

Dimitriyka Sakalieva

Keyword(s):

Molecular Characterization ◽

Reference Strain ◽

Rflp Analysis ◽

Plant Diseases ◽

Vegetable Crops ◽

Disease Symptoms ◽

Natural Plant ◽

Conserved Genes ◽

Reference Strains

Tomato and pepper are the main vegetable crops cultivated in Bulgaria. Phytoplasma diseases, mainly stolbur, are important plant diseases for these crops in Bulgaria. The goal of the present paper was to verify association of phytoplasmas with the observed disease symptoms in tomato and pepper and to identify the phytoplasmas detected using RFLP analysis of conserved genes and other uncharacterised phytoplasma chromosomal regions. The presence of phytoplasmas was confirmed in all the samples of tomato and pepper showing typical stolbur symptoms. A phytoplasm sample, which caused severe symptoms, showed the same pattern as the reference strain Mol, while all other phytoplasmic reference strains showed different polymorphisms. RFLP profiles were found useful in distinguishing phytoplasmas in stolbur subgroup (16SrXII-A) in natural plant hosts.

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First Isolation and Molecular Characterization of Chicken Astrovirus and Avian Nephritis Virus in Chickens in Bangladesh

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.769489 ◽

2021 ◽

Vol 8 ◽

Author(s):

Md Zulfekar Ali ◽

Mohammad Moktader Moula ◽

Zafar Ahmed Bhuiyan ◽

Md Giasuddin ◽

Hyun-Jin Shin

Keyword(s):

Phylogenetic Analysis ◽

Molecular Characterization ◽

Economic Damage ◽

Specific Pathogen Free ◽

Avian Nephritis Virus ◽

Wide Range ◽

Specific Pathogen ◽

Reference Strains ◽

Virus Screening

Chicken astrovirus (CAstV) and avian nephritis virus (ANV) are enteric viruses of poultry and have infected a wide range of poultry species worldwide, causing runting-stunting syndrome (RSS), which requires virus screening and results in serious economic damage. No confirmed cases have been reported from Bangladesh. In the present study, CAstV and ANV were monitored in Bangladesh. We monitored samples for CAstV and ANV and compared their genomic sequences to other reference strains. We found 8/31 flocks (25.8%) were positive for CAstV, 6/31 flocks (19.3%) had mixed infection of CAstV and ANV, and 1 flock (3.2%) was positive for ANV. Only ANV and a combination of CAstV and ANV were found in broilers and broiler breeders, but CAstV was found in all types of chickens. We isolated two of each from CAstV and ANV through specific pathogen-free chicken embryonated eggs via the yolk sac route. Phylogenetic analysis based on the ORF1b conserved region of CAstV and ANV suggested that the locally circulating strain was closely related to the strains isolated from India and Brazil. This report is the first molecular characterization of CAstV and ANV in Bangladesh. This study highlights that CAstV and ANV are circulating in Bangladeshi poultry.

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Schistura obliquofascia, a new loach from Uttarakhand, India (Cypriniformes: Nemacheilidae)

Zootaxa ◽

10.11646/zootaxa.3586.1.24 ◽

2012 ◽

Vol 3586 (1) ◽

pp. 255 ◽

Cited By ~ 2

Author(s):

Y. LOKESHWOR ◽

A. BARAT ◽

J. SATI ◽

A. DARSHAN ◽

W. VISHWANATH ◽

...

Keyword(s):

New Species ◽

Molecular Characterization ◽

Mandibular Canal ◽

The Body ◽

Base Pairs ◽

Ganga Basin ◽

Dorsal Fin ◽

Black Spots ◽

River Ganga

A new nemacheilid loach, Schistura obliquofascia, is described from Kalsa, a stream near Chanfi, tributary of Gola River,Ganga basin in Uttarakhand, India. The new species is readily distinguished from congeners by the following combinationof characters: 12–14 oblique olivaceous dark bars on the body and three rows of black spots on the dorsal fin; lateral linecomplete with 104–112 pores, dorsal fin with 3–4 simple and 8½ branched rays; 8+8 branched rays in caudal fin; dorsaladipose crest prominent; males lacking suborbital flap; and 10–11 pores in preoperculo-mandibular canal. The sequence of the cytochrome b gene of length 307 base pairs was used for molecular characterization of the species.

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Molecular characterization of watermelon cultivars using microsatellite markers

Horticultura Brasileira ◽

10.1590/s0102-05362013000400003 ◽

2013 ◽

Vol 31 (4) ◽

pp. 522-527 ◽

Cited By ~ 1

Author(s):

Renata Natália CS Gama ◽

Carlos Antônio F Santos ◽

Rita de Cássia S Dias ◽

Flávio F Souza

Keyword(s):

Microsatellite Markers ◽

Microsatellite Loci ◽

Genetic Similarity ◽

Group Method ◽

Reaction Products ◽

Base Pairs ◽

Arithmetic Means ◽

Pair Group ◽

Total Dna

Allelic patterns and genetic similarity among 17 watermelon cultivars were established using microsatellite markers. For visualization of the genetic similarity, the dendrogram UPGMA (Unweighted Pair Group Method with Arithmetic Means) was generated by the similarity matrix of the Jacquard coefficient, based on 34 alleles of ten microsatellite loci. Total DNA was extracted by the CTAB 2x method and PCR (Polymerase Chain Reaction) products were analyzed in denaturing polyacrylamide 6% gels, stained with silver nitrate. The number of base pairs was estimated by the method of inverse mobility, based on known size product regression. Similarity ranged from 34 to 100%, reflecting high genetic variability. Analyzed loci were not enough to distinguish all 17 watermelon cultivars. The pairs 'Sugar Baby' and 'Omaru Yamato', 'Charleston Gray' and 'Sunshade', 'Crimson Sweet' and 'Nova Crimson' presented 100% of similarity. In dendrogram two groups were observed at 0.42 similarity cut point, with Citrullus colocynthis, positioned as an out group. One watermelon group was formed predominantly by cultivars derived from 'Crimson' and another group was formed by cultivars of different types such as 'Sugar Baby', 'Charleston Gray' and 'Pérola'. Allele pattern and base pair (bp) estimates for the 34 alleles in the 10 microsatellite loci revealed in the present study are a first endeavor to use microsatellite markers in situations of cultivar protection for the watermelon agribusiness in Brazil. They can also be used in situations of commercial disputes regarding certification of the main watermelon cultivars used in the country.

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Molecular Characterization of Five Medicinally Important Species of Typhonium (Araceae) through Random Amplified Polymorphic DNA (RAPD)

Zeitschrift für Naturforschung C ◽

10.1515/znc-2005-7-815 ◽

2005 ◽

Vol 60 (7-8) ◽

pp. 600-604 ◽

Cited By ~ 5

Author(s):

Laxmikanta Acharya ◽

Arup Kumar Mukherjee ◽

Pratap Chandra Panda ◽

Premananda Das

Keyword(s):

Molecular Characterization ◽

Genetic Similarity ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Similarity Index ◽

The Other ◽

Important Species ◽

Species Specific ◽

Maximum Similarity

The interrelationship of five medicinally important species of Typhonium (Araceae) including T. venosum, which was previously placed under the genus Sauromatum, was inferred by analysis of random amplified polymorphic DNA (RAPD). DNA from pooled leaf samples was isolated and RAPD analysis was performed using 20 decamer oligonucleotide primers. Out of a total of 245 bands amplified, 12 were found to be monomorphic while 233 bands were polymorphic including 86 species-specific bands. The genetic similarities were analyzed from the dendrogram constructed by the pooled RAPD data using a similarity index. The dendrogram showed two distinct clades, one containing T. roxburghii, T. trilobatum and T. venosum and the other containing the remainder two species, i.e. T. diversifolium and T. flagelliforme. Both the clusters shared a common node approx. at 23.7% level of similarity. The maximum similarity of 31.2% was observed between T. venosum and T. trilobatum. In view of its close genetic similarity with other members of Typhonium, transfer of Sauromatum venosum to the genus Typhonium and merger of the two genera was supported.

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