Development of a PCR protocol for the identification and detection of Fusarium solani f. sp. piperis from soil and roots ... View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2017-01-24

AUTHORS

Sarah S. Costa, Gláucia M. Moreira, Ludwig H. Pfenning

ABSTRACT

The main disease of black pepper (Piper nigrum) in Brazil is caused by Fusarium solani f. sp. piperis. The disease diagnosis is problematic because, besides this pathogen, there are other different phylogenetic lineages within the Fusarium solani species complex (FSSC) associated with black pepper that can not be reliably identified based solely on morphological characteristics. Based on differences in the translation elongation factor 1-alpha (EF-1α) gene sequences of species of the FSSC, one pair of species-specific primers, Fpiper1F/Fpiper1R, was synthesized to accurately detect and identify F. solani f. sp. piperis. Primer specificity was tested with DNA from 18 isolates of F. solani f. sp. piperis, 24 representative isolates of other lineages of the FSSC associated with P. nigrum, and isolates representing eight strains of other species. The primers amplified only a single PCR band of 230 bp from F. solani f. sp. piperis. Nested PCR was more sensitive than conventional PCR, using the primer pair EF1/EF2 for the first round and specific primers Fpiper1F/Fpiper1R for the second round. Detection sensitivity was 1 fg of purified F. solani f. sp. piperis DNA template and 101 macroconidia/g soil infected. The specific primers will greatly facilitate the detection and identification of F. solani f. sp. piperis, and have potential as a diagnostic tool for detecting this pathogen in field-grown black pepper soil. More... »

PAGES

55-59

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s40858-016-0124-2

DOI

http://dx.doi.org/10.1007/s40858-016-0124-2

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1074202390


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Dep. de Fitopatologia, Universidade Federal de Lavras, CP 3037, 37200-000, Lavras, MG, Brazil", 
          "id": "http://www.grid.ac/institutes/grid.411269.9", 
          "name": [
            "Dep. de Fitopatologia, Universidade Federal de Lavras, CP 3037, 37200-000, Lavras, MG, Brazil"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Costa", 
        "givenName": "Sarah S.", 
        "id": "sg:person.01307456315.54", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01307456315.54"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Dep. de Fitopatologia, Universidade Federal de Lavras, CP 3037, 37200-000, Lavras, MG, Brazil", 
          "id": "http://www.grid.ac/institutes/grid.411269.9", 
          "name": [
            "Dep. de Fitopatologia, Universidade Federal de Lavras, CP 3037, 37200-000, Lavras, MG, Brazil"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Moreira", 
        "givenName": "Gl\u00e1ucia M.", 
        "id": "sg:person.014630263303.48", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014630263303.48"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Dep. de Fitopatologia, Universidade Federal de Lavras, CP 3037, 37200-000, Lavras, MG, Brazil", 
          "id": "http://www.grid.ac/institutes/grid.411269.9", 
          "name": [
            "Dep. de Fitopatologia, Universidade Federal de Lavras, CP 3037, 37200-000, Lavras, MG, Brazil"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pfenning", 
        "givenName": "Ludwig H.", 
        "id": "sg:person.016626703577.84", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016626703577.84"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1023/a:1021208106857", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042765343", 
          "https://doi.org/10.1023/a:1021208106857"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2017-01-24", 
    "datePublishedReg": "2017-01-24", 
    "description": "The main disease of black pepper (Piper nigrum) in Brazil is caused by Fusarium solani f. sp. piperis. The disease diagnosis is problematic because, besides this pathogen, there are other different phylogenetic lineages within the Fusarium solani species complex (FSSC) associated with black pepper that can not be reliably identified based solely on morphological characteristics. Based on differences in the translation elongation factor 1-alpha (EF-1\u03b1) gene sequences of species of the FSSC, one pair of species-specific primers, Fpiper1F/Fpiper1R, was synthesized to accurately detect and identify F. solani f. sp. piperis. Primer specificity was tested with DNA from 18 isolates of F. solani f. sp. piperis, 24 representative isolates of other lineages of the FSSC associated with P. nigrum, and isolates representing eight strains of other species. The primers amplified only a single PCR band of 230\u00a0bp from F. solani f. sp. piperis. Nested PCR was more sensitive than conventional PCR, using the primer pair EF1/EF2 for the first round and specific primers Fpiper1F/Fpiper1R for the second round. Detection sensitivity was 1\u00a0fg of purified F. solani f. sp. piperis DNA template and 101 macroconidia/g soil infected. The specific primers will greatly facilitate the detection and identification of F. solani f. sp. piperis, and have potential as a diagnostic tool for detecting this pathogen in field-grown black pepper soil.", 
    "genre": "article", 
    "id": "sg:pub.10.1007/s40858-016-0124-2", 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1381338", 
        "issn": [
          "1982-5676", 
          "1678-4677"
        ], 
        "name": "Tropical Plant Pathology", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "42"
      }
    ], 
    "keywords": [
      "F. solani f.", 
      "solani f.", 
      "Fusarium solani f.", 
      "primer pairs EF1/EF2", 
      "translation elongation factor", 
      "different phylogenetic lineages", 
      "Fusarium solani species", 
      "single PCR band", 
      "species-specific primers", 
      "EF1/EF2", 
      "phylogenetic lineages", 
      "elongation factor", 
      "gene sequences", 
      "Primer specificity", 
      "DNA template", 
      "piperis", 
      "representative isolates", 
      "species", 
      "black pepper", 
      "f.", 
      "lineages", 
      "PCR bands", 
      "specific primers", 
      "primers", 
      "morphological characteristics", 
      "PCR protocol", 
      "macroconidia/", 
      "FSSC", 
      "pepper", 
      "pathogens", 
      "P. nigrum", 
      "conventional PCR", 
      "PCR", 
      "isolates", 
      "soil", 
      "Nested PCR", 
      "DNA", 
      "identification", 
      "EF2", 
      "nigrum", 
      "BP", 
      "detection sensitivity", 
      "sequence", 
      "roots", 
      "disease diagnosis", 
      "main disease", 
      "strains", 
      "specificity", 
      "second round", 
      "Brazil", 
      "detection", 
      "pairs", 
      "template", 
      "development", 
      "diagnostic tool", 
      "rounds", 
      "protocol", 
      "factors", 
      "potential", 
      "band", 
      "disease", 
      "tool", 
      "differences", 
      "sensitivity", 
      "characteristics", 
      "diagnosis"
    ], 
    "name": "Development of a PCR protocol for the identification and detection of Fusarium solani f. sp. piperis from soil and roots of black pepper (Piper nigrum)", 
    "pagination": "55-59", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1074202390"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s40858-016-0124-2"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s40858-016-0124-2", 
      "https://app.dimensions.ai/details/publication/pub.1074202390"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-08-04T17:05", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220804/entities/gbq_results/article/article_721.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1007/s40858-016-0124-2"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s40858-016-0124-2'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s40858-016-0124-2'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s40858-016-0124-2'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s40858-016-0124-2'


 

This table displays all metadata directly associated to this object as RDF triples.

141 TRIPLES      21 PREDICATES      91 URIs      82 LITERALS      6 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s40858-016-0124-2 schema:about anzsrc-for:06
2 anzsrc-for:0604
3 schema:author Neffbe7b9c37842feaa02ae07b5cac9aa
4 schema:citation sg:pub.10.1023/a:1021208106857
5 schema:datePublished 2017-01-24
6 schema:datePublishedReg 2017-01-24
7 schema:description The main disease of black pepper (Piper nigrum) in Brazil is caused by Fusarium solani f. sp. piperis. The disease diagnosis is problematic because, besides this pathogen, there are other different phylogenetic lineages within the Fusarium solani species complex (FSSC) associated with black pepper that can not be reliably identified based solely on morphological characteristics. Based on differences in the translation elongation factor 1-alpha (EF-1α) gene sequences of species of the FSSC, one pair of species-specific primers, Fpiper1F/Fpiper1R, was synthesized to accurately detect and identify F. solani f. sp. piperis. Primer specificity was tested with DNA from 18 isolates of F. solani f. sp. piperis, 24 representative isolates of other lineages of the FSSC associated with P. nigrum, and isolates representing eight strains of other species. The primers amplified only a single PCR band of 230 bp from F. solani f. sp. piperis. Nested PCR was more sensitive than conventional PCR, using the primer pair EF1/EF2 for the first round and specific primers Fpiper1F/Fpiper1R for the second round. Detection sensitivity was 1 fg of purified F. solani f. sp. piperis DNA template and 101 macroconidia/g soil infected. The specific primers will greatly facilitate the detection and identification of F. solani f. sp. piperis, and have potential as a diagnostic tool for detecting this pathogen in field-grown black pepper soil.
8 schema:genre article
9 schema:isAccessibleForFree false
10 schema:isPartOf N4f96cf83332a4e748cec1941fe82a4cc
11 Ne362264d408745de9e74a926d6a06988
12 sg:journal.1381338
13 schema:keywords BP
14 Brazil
15 DNA
16 DNA template
17 EF1/EF2
18 EF2
19 F. solani f.
20 FSSC
21 Fusarium solani f.
22 Fusarium solani species
23 Nested PCR
24 P. nigrum
25 PCR
26 PCR bands
27 PCR protocol
28 Primer specificity
29 band
30 black pepper
31 characteristics
32 conventional PCR
33 detection
34 detection sensitivity
35 development
36 diagnosis
37 diagnostic tool
38 differences
39 different phylogenetic lineages
40 disease
41 disease diagnosis
42 elongation factor
43 f.
44 factors
45 gene sequences
46 identification
47 isolates
48 lineages
49 macroconidia/
50 main disease
51 morphological characteristics
52 nigrum
53 pairs
54 pathogens
55 pepper
56 phylogenetic lineages
57 piperis
58 potential
59 primer pairs EF1/EF2
60 primers
61 protocol
62 representative isolates
63 roots
64 rounds
65 second round
66 sensitivity
67 sequence
68 single PCR band
69 soil
70 solani f.
71 species
72 species-specific primers
73 specific primers
74 specificity
75 strains
76 template
77 tool
78 translation elongation factor
79 schema:name Development of a PCR protocol for the identification and detection of Fusarium solani f. sp. piperis from soil and roots of black pepper (Piper nigrum)
80 schema:pagination 55-59
81 schema:productId N1b5b944a36bd45859ff294648d0817ba
82 Ne29fc873340e457085c275c553ba6f99
83 schema:sameAs https://app.dimensions.ai/details/publication/pub.1074202390
84 https://doi.org/10.1007/s40858-016-0124-2
85 schema:sdDatePublished 2022-08-04T17:05
86 schema:sdLicense https://scigraph.springernature.com/explorer/license/
87 schema:sdPublisher N409c55404d844894a51feb5d241bb41e
88 schema:url https://doi.org/10.1007/s40858-016-0124-2
89 sgo:license sg:explorer/license/
90 sgo:sdDataset articles
91 rdf:type schema:ScholarlyArticle
92 N1b5b944a36bd45859ff294648d0817ba schema:name dimensions_id
93 schema:value pub.1074202390
94 rdf:type schema:PropertyValue
95 N409c55404d844894a51feb5d241bb41e schema:name Springer Nature - SN SciGraph project
96 rdf:type schema:Organization
97 N4f96cf83332a4e748cec1941fe82a4cc schema:issueNumber 1
98 rdf:type schema:PublicationIssue
99 Nb82988d1021f43858e4cb510977b0286 rdf:first sg:person.016626703577.84
100 rdf:rest rdf:nil
101 Ne29fc873340e457085c275c553ba6f99 schema:name doi
102 schema:value 10.1007/s40858-016-0124-2
103 rdf:type schema:PropertyValue
104 Ne362264d408745de9e74a926d6a06988 schema:volumeNumber 42
105 rdf:type schema:PublicationVolume
106 Neffbe7b9c37842feaa02ae07b5cac9aa rdf:first sg:person.01307456315.54
107 rdf:rest Nf5ba9eb5cc2447338e9f901cbf498510
108 Nf5ba9eb5cc2447338e9f901cbf498510 rdf:first sg:person.014630263303.48
109 rdf:rest Nb82988d1021f43858e4cb510977b0286
110 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
111 schema:name Biological Sciences
112 rdf:type schema:DefinedTerm
113 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
114 schema:name Genetics
115 rdf:type schema:DefinedTerm
116 sg:journal.1381338 schema:issn 1678-4677
117 1982-5676
118 schema:name Tropical Plant Pathology
119 schema:publisher Springer Nature
120 rdf:type schema:Periodical
121 sg:person.01307456315.54 schema:affiliation grid-institutes:grid.411269.9
122 schema:familyName Costa
123 schema:givenName Sarah S.
124 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01307456315.54
125 rdf:type schema:Person
126 sg:person.014630263303.48 schema:affiliation grid-institutes:grid.411269.9
127 schema:familyName Moreira
128 schema:givenName Gláucia M.
129 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014630263303.48
130 rdf:type schema:Person
131 sg:person.016626703577.84 schema:affiliation grid-institutes:grid.411269.9
132 schema:familyName Pfenning
133 schema:givenName Ludwig H.
134 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016626703577.84
135 rdf:type schema:Person
136 sg:pub.10.1023/a:1021208106857 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042765343
137 https://doi.org/10.1023/a:1021208106857
138 rdf:type schema:CreativeWork
139 grid-institutes:grid.411269.9 schema:alternateName Dep. de Fitopatologia, Universidade Federal de Lavras, CP 3037, 37200-000, Lavras, MG, Brazil
140 schema:name Dep. de Fitopatologia, Universidade Federal de Lavras, CP 3037, 37200-000, Lavras, MG, Brazil
141 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...