RFLP and Rapd Analyses in the Identification and Differentiation of Isolates of the Leaf Spot Fungus Corynespora cassiicola

1995 ◽  
Vol 43 (6) ◽  
pp. 609 ◽  
Author(s):  
WPK Silva ◽  
DS Multani ◽  
BJ Deverall ◽  
BR Lyon

Genetic variabilty in isolates of the fungal plant pathogen Corynespora cassiicola cultured from pawpaw, mimosa and thyme hosts was assessed using restriction fragment length polymorphism (RFLP) analysis of internal transcribed spacer (ITS) regions of ribosomal DNA and random amplified polymorphic DNA (RAPD) analysis of total fungal DNA. Strains of Corynespora could be distinguished from a member of the closely-related genus Helminthosporium on the basis of amplified ITS fragment size, but could not be typed individually as the ITS regions of all isolates exhibited identical size and restriction endonuclease digestion pattern. However, RAPD profiles generated by 14 decamer primers of arbitrary sequence did reveal significant differences between some of the C. cassiicola isolates and succeeded in differentiating all but two of the strains. Cluster analysis of 218 amplified DNA fragments showed that the five isolates could be placed into three groups that correspond with their host origin and morphological characteristics. The use of these molecular techniques will be extended to assess intra-specific variation in C. cassiicola isolates from rubber trees in Sri Lanka, where highly pathogenic strains present a serious threat to the natural rubber industry.

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 51-58 ◽  
Author(s):  
K K Nkongolo ◽  
P Michael ◽  
W S Gratton

Total genomic DNAs were extracted from several populations of pine species and amplified using oligonucleotides of random sequences. Polymorphism in random amplified polymorphic DNA (RAPD) markers was high and sufficient in distinguishing each of the species. Genetic relationships among eight pine species (Pinus sylvestris, Pinus strobus, Pinus rigida, Pinus resinosa, Pinus nigra, Pinus contorta, Pinus monticola, and Pinus banksiana) from different provenances were analyzed. The degree of band sharing was used to evaluate genetic distance between species and to construct a phylogenetic tree. In general, the dendrogram corroborated the description of relationships based on morphological characteristics and crossability, but also provided new insights into pine taxonomy. RAPD markers specific to some pine species were cloned and sequenced. PCR amplifications using pairs of designed specific primers revealed that all the cloned sequences were likely genus specific because they were not found in spruce or larch. True species-specific sequences were identified using designed primers flanking cloned RAPD fragments. The analysis of RAPD fragment sequences confirmed the genetic relationships among species. A 2281-bp RAPD band called PI-Mt-Stb-23 from P. strobus was used as a probe in restriction fragment length polymorphism (RFLP) analysis and produced distinct banding patterns for each species examined, consistent with the highly polymorphic character of DNA-fingerprinting probes.Key words: Pine, RAPD, RFLP, cloning, species-specific sequences.


Author(s):  
Gabriella Vindigni ◽  
Alfredo Pulvirenti ◽  
Salvatore Alaimo ◽  
Clara Monaco ◽  
Daniela Spina ◽  
...  

Fisheries products are some of the most traded commodities world-wide and the potential for fraud is a serious concern. Fish fraud represents a threat to human health and poses serious concerns due to the consumption of toxins, highly allergenic species, contaminates or zoonotic parasites, which may be present in substituted fish. The substitution of more expensive fish by cheaper species, with similar morphological characteristics but different origins, reflects the need for greater transparency and traceability upon which which the security of the entire seafood value-chain depends. Even though EU regulations have made significant progress in consumer information by stringent labelling requirements, fraud is still widespread. Many molecular techniques such as DNA barcoding provide valuable support to enhance the Common Fisheries Policy (CFP) in the protection of consumer interests by unequivocally detecting any kind of fraud. This paper aims to highlight both the engagement of EU fishery policy and the opportunity offered by new biotechnology instruments to mitigate the growing fraud in the globalized fish market and to enforce the food security system to protect consumers’ health. In this paper, after a presentation of EU rules on fish labeling and a general overview on the current state of the global fish market, we discuss the public health implications and the opportunities offered by several techniques based on genetics, reporting a case study to show the efficacy of the DNA barcoding methodology in assessing fish traceability and identification, comparing different species of the Epinephelus genus, Mottled Grouper (Mycteroperca rubra) and Wreckfish (Polyprion americanus), often improperly sold with the commercial name of “grouper”.


2019 ◽  
Vol 7 (1) ◽  
pp. 12 ◽  
Author(s):  
O-Chul Kwon ◽  
Chang-Soo Lee ◽  
Young-Jin Park

In this study we identified single nucleotide polymorphism (SNP) and sequence characteristic amplification region (SCAR) markers for specific identification of antler-shaped Ganoderma lucidum strains. When the partial mitochondrial SSU rDNA gene sequence of various antler- and kidney-shaped G. lucidum strains were analyzed and aligned, an SNP was found only in the antler-shaped G. lucidum strain at position 456 bp. In addition, this SNP of antler-shaped strains was digested by HinfI restriction enzyme. We further analyzed the polymorphism of various G. lucidum strains by random amplified polymorphic DNA (RAPD) analysis. In RAPD analysis, we isolated and sequenced a fragment, specific for antler-shaped G. lucidum strains. Based on this specific fragment sequence, two sets of specific primer pairs for antler-shaped G. lucidum strains were designed. PCR analysis revealed that two specific bands were observed only from antler-shaped strains. These two molecular markers will be helpful for identification of morphological characteristics of G. lucidum.


Botany ◽  
2012 ◽  
Vol 90 (9) ◽  
pp. 866-875 ◽  
Author(s):  
Deana L. Baucom ◽  
Marie Romero ◽  
Robert Belfon ◽  
Rebecca Creamer

New species of Undifilum , from locoweeds Astragalus lentiginosus Vitman and Astragalus mollissimus Torr., are described using morphological characteristics and molecular phylogenetic analyses as Undifilum fulvum Baucom & Creamer sp. nov. and Undifilum cinereum Baucom & Creamer sp. nov. Fungi were isolated from dried plants of A. lentiginosus var. araneosus , diphysus , lentiginosus , and wahweapensis collected from Arizona, Oregon, and Utah, USA, and A. mollissimus var. biglovii , earleii , and mollissimus collected from New Mexico, Oklahoma, and Texas, USA. Endophytic fungi from Astragalus locoweeds were compared to Undifilum oxytropis isolates obtained from dried plant material of Oxytropis lamberteii from New Mexico and Oxytropis sericea from Arizona, Colorado, New Mexico, Utah, and Wyoming. Extremely slow growth in vitro was observed for all, and conidia, if present, were ellipsoid with transverse septa. However, in vitro color, growth on four different media, and conidium size differed between fungi from Astragalus spp. and U. oxytropis. Neighbor-joining analyses of internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GPD) gene sequences revealed that U. fulvum and U. cinereum formed a clade distinct from U. oxytropis. This was supported by neighbor-joining analyses of results generated from random amplified polymorphic DNA (RAPD) fragments using two different primers.


Plant Disease ◽  
2014 ◽  
Vol 98 (11) ◽  
pp. 1586-1586 ◽  
Author(s):  
G. Q. Yuan ◽  
Y. L. Xie ◽  
D. C. Tan ◽  
Q. Q. Li ◽  
W. Lin

Kiwifruit (Actinidia) is a common fruit cultivated in many countries. Actinidia deliciosa and A. chinensis are two commercially important kiwifruit species. Over 70,000 ha are grown annually in China. In 2012, a leaf spot disease of A. chinensis was observed in several orchards in Leye County (106°34′ E, 24°47′ N), Guangxi Zhuang Autonomous Region, China. The disease mainly damaged the leaves during the fruit development stage through to the maturity stage. Initially reddish-brown small lesions appeared on the leaves; later, typical symptoms were tan to taupe lesions surrounded by purple brown margins, nearly circular to irregular, 2 to 10 × 2.2 to 15.5 mm in diameter. Some lesions exhibited a concentric pattern. The lesions eventually coalesced, causing extensive leaf necrosis and defoliation. The fungus that sporulated from lesions had the following morphological characteristics: light brown conidiophores with slightly swollen apexes, light brown conidia formed singly or in acropetal chains, straight or curved, cylindrical to oblavate, 52.9 to 240.5 μm long (avg. 138.9 μm) and 5.3 to 13.6 μm wide (avg. 8.4 μm), 5 to 12 distoseptate, with a flat, darkened, and thickened hilum. These morphological characteristics corresponded with that of Corynespora cassiicola (Berk. & Curt.) Wei (1). To isolate the pathogen of the disease, small pieces of symptomatic foliar tissues, including young lesions, typical older lesions, and atypical older lesions with concentric pattern were surface sterilized with 75% ethanol for 30 to 60 s, disinfected in 0.1% HgCl2 for 1 min followed by washing with sterile water, plated on PDA, and incubated at 28°C for 7 to 10 days. Gray to dark gray colonies and conidia of C. cassiicola were observed. To validate the identity of the fungus, the sequence of the ITS region of one of the purified strains, LYCc-1, was determined. DNA was extracted from the isolate that was grown on PDA at 28°C for 4 days, and the ITS region was amplified using the universal primer pair ITS4/ITS5 (2). The double strand consensus sequence was submitted to GenBank (KJ747095) and had 99% nt identity with published sequences of C. cassiicola in GenBank (JN853778, FJ852574, and FJ852587). Pathogenicity tests were carried out on detached leaves in petri dishes in an incubator at 28°C and on whole plants in a glasshouse at 25 ± 3°C. The isolations did not produce enough conidia in pure culture, so mycelial discs were used in pathogenicity tests. For both assays, 60-day-old healthy kiwifruit leaves were inoculated with a 5-mm mycelial disc obtained from the periphery of a 5-day-old C. cassiicola strain (LYCc-1) grown on PDA. The PDA discs were placed on the leaf surface with their mycelial surface down and secured with sterile wet cotton. Controls consisted of leaves that were inoculated with sterile PDA discs. For the detached leaf assay, the leaves were placed on filter paper reaching water saturation in petri dishes, and for the whole plant assays the inoculated leaves were kept moist with intermittent water sprays for 48 h. Four leaves of each plant were inoculated with the isolate in both assays, and experiment was repeated twice. Eight inoculated leaves of the detached leaf assay all showed the first water soaked lesions 36 h after inoculation, followed by extensive leaf rot 72 h after inoculation, and yielded abundant conidia of C. cassiicola. Six out of eight leaves inoculated on whole plants showed the first lesions 5 days after inoculation, whereas control leaves remained healthy. Only C. cassiicola was re-isolated from the lesions in both assays, fulfilling Koch's postulates. This is the first report of leaf spot caused by C. cassiicola on kiwifruit in China. References: (1) M. B. Ellis. Dematiaceous Hyphomycetes. CMI, Kew, Surrey, UK, 1971. (2) T. J. White et al. In: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990.


2017 ◽  
Vol 18 ◽  
pp. 56 ◽  
Author(s):  
Ioannis Th. Anagnostopoulos

From the study of the Greek bumblebee fauna (Hymenoptera: Apidae, Bombini), species lists have been published based on both literature records and original data from collected bees. Since 1995 a special effort to confirm with newly collected bees all bumblebee species reported in literature records for Greece has been in progress. Although numerous specimens have been collected and examined and in some instances yielding new Bombus species for the Greek insect fauna, some species, mainly those reported in older references, have not yet been found. Recently, identification of bumblebees collected in the Florina Prefecture - Northwest Macedonia, during the years 2006 and 2007 yielded information for two “literature cited” species, Bombus subterraneus (Linnaeus 1758) and Bombus cryptarum (Fabricius 1775). A B. subterraneus queen (collected at 40°47´38N, 21°26´10E on Vicia cracca) was distinguished by morphological characteristics and a worker B. cryptarum (collected at 40°41´58,7N, 21°28´18,5E on Echium spp) was revealed using mitochondrial DNA RFLP analysis of the CO1 gene. These new records from Florina are provided with comments, confirming the species presence in Greece for the first time after approximately 40 years.


Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 580
Author(s):  
Hongyi Liu ◽  
Yufeng Zhang ◽  
Wei Xu ◽  
Yu Fang ◽  
Honghua Ruan

Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus, Dendrobaena octaedra, Eisenia andrei, Eisenia nordenskioldi, and Octolasion tyrtaeum) with lengths ranging from 14,977 to 15,715 were presented. Each mitogenome possessed a putative control region that resided between tRNA-Arg and tRNA-His. All of the PCGs were under negative selection according to the value of Ka/Ks. The phylogenetic trees supported the classification of Eisenia and Lumbricus; however, the trees based on cox1 did not. Through various comparisons, it was determined that cox1 fragments might be more suitable for molecular identification. These results lay the foundation for further phylogenetic studies on Lumbricidae.


Author(s):  
Fidia Fibriana ◽  
Lutfia Nur Hadiyanti

<p>In this study, twenty local durian accessions obtained from Central Java in situ collection were characterized using the morphological characteristics and the restriction patterns which generated from the region spanning the internal transcribed spacers ITS LEU and ITS 4. Morphological characteristics of durian leaf, stem, tree, and fruit showed variations for the different accessions, whereas polymerase chain reaction (PCR) products of ribosomal DNA region showed a low length of variation. The size of the PCR products and the restriction analyses with the restriction endonucleases Bsp1431yielded a restriction pattern for each accessions. The results of this study can be utilized by local durian farmers as a preliminary reference for durian propagation. The data obtained need to be supported by further research using the other molecular markers to obtain more accurate data. The clear identity of durian species can help the management of propagation systems by farmers to get superior local durian.</p><p><strong>How to Cite</strong></p><p>Fibriana, F., &amp; Hadiyanti, L. N. (2016). Phylogenetic Relationships of Local Durian Species based on Morphological Characteristics and PCR-RFLP Analysis of the Ribosomal Internal Transcribed Spacer (ITS) DNA. <em>Biosaintifika: Journal of Biology &amp; Biology Education</em>, 8(3), 362-370. </p>


HortScience ◽  
2018 ◽  
Vol 53 (9) ◽  
pp. 1266-1270 ◽  
Author(s):  
Nader R. Abdelsalam ◽  
Hayssam M. Ali ◽  
Mohamed Z.M. Salem ◽  
Elsayed G. Ibrahem ◽  
Mohamed S. Elshikh

Mango (Mangifera indica L.) is a fruit crops belong to the family Anacardiaceae and is the oldest cultivated tree worldwide. Cultivars maintained in Egypt have not been investigated previously. Mango was first brought to Egypt from South Asia. Morphological and molecular techniques were used to identify the genetic diversity within 28 mango cultivars. SSR and EST-SSR were used for optimizing germplasm management of mango cultivars. Significant variations were observed in morphological characteristics and genetic polymorphism, as they ranged from 0.71% to 100%. High diversity was confirmed as a pattern of morphological and genotypes data. Data from the present study may be used to calculate the mango relationship and diversity currently grown in Egypt.


Phytotaxa ◽  
2017 ◽  
Vol 298 (1) ◽  
pp. 20 ◽  
Author(s):  
YUAN YUAN ◽  
XIAO-HONG JI ◽  
FANG WU ◽  
JIA-JIA CHEN

A new polypore, Ceriporia albomellea, collected from tropical China, is described and illustrated based on morphological characteristics and molecular evidence. It is characterized by thin, resupinate basidiome with a white subiculum, cottony margin, white to cinnamon-buff pores, clavate cystidia and oblong-ellipsoid basidiospores measured as 3.1–3.8 × 1.7–2 µm. Phylogenetic analysis based on the internal transcribed spacer (ITS) regions and nuclear large subunit (nLSU) ribosomal RNA gene regions supported C. albomellea as a distinctive species belonging to Ceriporia.


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