Cross amplification of 16S rRNA bacterial primer 27F/1492R on horticultural crop chloroplast genome
Molecular techniques have been applied as fast and accurate detection methods of plant pathogenic bacteria. Bacteria-specific primer 27F paired with the universal primer 1492R was used in PCR to detect plant pathogenic bacteria in symptomatic leaves of tomato (Solanum lycopersicum L.), chili pepper...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Faculty of Agriculture, Merdeka University Surabaya
2024-03-01
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| Series: | Agricultural Science |
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| Online Access: | https://agriculturalscience.unmerbaya.ac.id/index.php/agriscience/article/view/132 |
| _version_ | 1797226735829254144 |
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| author | Adyatma Irawan Santosa Taufiq Hilmany Nurul Aulia Dewi Novianti Ekaputri Rahmawati Erika Ananda Putri Tiara Hafidsya Ary Virgianti Setyaningrum Rulia Ervina Dewi Gracela Nanda Puspita Sari Mars Buwn Fraset Manao Nubatonis Arya Widyawan |
| author_facet | Adyatma Irawan Santosa Taufiq Hilmany Nurul Aulia Dewi Novianti Ekaputri Rahmawati Erika Ananda Putri Tiara Hafidsya Ary Virgianti Setyaningrum Rulia Ervina Dewi Gracela Nanda Puspita Sari Mars Buwn Fraset Manao Nubatonis Arya Widyawan |
| author_sort | Adyatma Irawan Santosa |
| collection | DOAJ |
| description | Molecular techniques have been applied as fast and accurate detection methods of plant pathogenic bacteria. Bacteria-specific primer 27F paired with the universal primer 1492R was used in PCR to detect plant pathogenic bacteria in symptomatic leaves of tomato (Solanum lycopersicum L.), chili pepper (Capsicum annum L.), napa cabbage (Brassica rapa subsp. pekinensis L.), cabbage (Brassica oleracea var. capitata L.), and longan (Dimocarpus longan Lour.). The targeted single bands with length of 1400 bp were obtained but bidirectional sequencing of the PCR products recovered partial sequence of chloroplast instead of bacterial genomes. Thus, this result confirmed cross amplification of 27F/1492R primer pair against chloroplast genome of plants. Phylogenetic tree was constructed to separate the tested isolates according to their taxonomic relations: Order Sapindales, Solanales, and Brassicales. In-silico analysis on the new five and nineteen selected sequences in NCBI GenBank detected at least seven conserved regions with some single nucleotide polymorphisms. This report might be a cautionary advice for other researchers to avoid false positive results which could lead to misdiagnosis of bacterial plant diseases. |
| first_indexed | 2024-04-24T14:29:38Z |
| format | Article |
| id | doaj.art-09085dea39ae46cbb22cb104f6ad8160 |
| institution | Directory Open Access Journal |
| issn | 2598-5167 2597-8713 |
| language | English |
| last_indexed | 2024-04-24T14:29:38Z |
| publishDate | 2024-03-01 |
| publisher | Faculty of Agriculture, Merdeka University Surabaya |
| record_format | Article |
| series | Agricultural Science |
| spelling | doaj.art-09085dea39ae46cbb22cb104f6ad81602024-04-03T03:32:19ZengFaculty of Agriculture, Merdeka University SurabayaAgricultural Science2598-51672597-87132024-03-017217218310.55173/agriscience.v7i2.132132Cross amplification of 16S rRNA bacterial primer 27F/1492R on horticultural crop chloroplast genomeAdyatma Irawan Santosa0https://orcid.org/0000-0002-2826-5444Taufiq Hilmany1https://orcid.org/0000-0002-2826-5444Nurul Aulia Dewi2https://orcid.org/0009-0000-2195-2623Novianti Ekaputri Rahmawati3https://orcid.org/0009-0005-6735-6444Erika Ananda Putri4https://orcid.org/0009-0006-3301-0557Tiara Hafidsya5https://orcid.org/0009-0004-5985-1384Ary Virgianti Setyaningrum6https://orcid.org/0009-0007-1718-7210Rulia Ervina Dewi7https://orcid.org/0000-0002-1461-6266Gracela Nanda Puspita Sari8https://orcid.org/0009-0008-4202-0399Mars Buwn Fraset Manao Nubatonis9https://orcid.org/0009-0009-6897-8965Arya Widyawan10https://orcid.org/0000-0003-2208-3794Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah MadaDepartment of Plant Protection, Faculty of Agriculture, Universitas Gadjah MadaDepartment of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, novianti.ekaputri.r@mail.ugm.ac.idDepartment of Plant Protection, Faculty of Agriculture, Universitas Gadjah MadaDepartment of Plant Protection, Faculty of Agriculture, Universitas Gadjah MadaDepartment of Plant Protection, Faculty of Agriculture, Universitas Gadjah MadaDepartment of Plant Protection, Faculty of Agriculture, Universitas Gadjah MadaDepartment of Plant Protection, Faculty of Agriculture, Universitas Gadjah MadaDepartment of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada1) Plant Protection Department, College of Food and Agriculture Sciences, King Saud UniversityMolecular techniques have been applied as fast and accurate detection methods of plant pathogenic bacteria. Bacteria-specific primer 27F paired with the universal primer 1492R was used in PCR to detect plant pathogenic bacteria in symptomatic leaves of tomato (Solanum lycopersicum L.), chili pepper (Capsicum annum L.), napa cabbage (Brassica rapa subsp. pekinensis L.), cabbage (Brassica oleracea var. capitata L.), and longan (Dimocarpus longan Lour.). The targeted single bands with length of 1400 bp were obtained but bidirectional sequencing of the PCR products recovered partial sequence of chloroplast instead of bacterial genomes. Thus, this result confirmed cross amplification of 27F/1492R primer pair against chloroplast genome of plants. Phylogenetic tree was constructed to separate the tested isolates according to their taxonomic relations: Order Sapindales, Solanales, and Brassicales. In-silico analysis on the new five and nineteen selected sequences in NCBI GenBank detected at least seven conserved regions with some single nucleotide polymorphisms. This report might be a cautionary advice for other researchers to avoid false positive results which could lead to misdiagnosis of bacterial plant diseases.https://agriculturalscience.unmerbaya.ac.id/index.php/agriscience/article/view/132chloroplastmolecular detectionnucleotide polymorphismsphylogenetic tree16s ribosomal rna |
| spellingShingle | Adyatma Irawan Santosa Taufiq Hilmany Nurul Aulia Dewi Novianti Ekaputri Rahmawati Erika Ananda Putri Tiara Hafidsya Ary Virgianti Setyaningrum Rulia Ervina Dewi Gracela Nanda Puspita Sari Mars Buwn Fraset Manao Nubatonis Arya Widyawan Cross amplification of 16S rRNA bacterial primer 27F/1492R on horticultural crop chloroplast genome Agricultural Science chloroplast molecular detection nucleotide polymorphisms phylogenetic tree 16s ribosomal rna |
| title | Cross amplification of 16S rRNA bacterial primer 27F/1492R on horticultural crop chloroplast genome |
| title_full | Cross amplification of 16S rRNA bacterial primer 27F/1492R on horticultural crop chloroplast genome |
| title_fullStr | Cross amplification of 16S rRNA bacterial primer 27F/1492R on horticultural crop chloroplast genome |
| title_full_unstemmed | Cross amplification of 16S rRNA bacterial primer 27F/1492R on horticultural crop chloroplast genome |
| title_short | Cross amplification of 16S rRNA bacterial primer 27F/1492R on horticultural crop chloroplast genome |
| title_sort | cross amplification of 16s rrna bacterial primer 27f 1492r on horticultural crop chloroplast genome |
| topic | chloroplast molecular detection nucleotide polymorphisms phylogenetic tree 16s ribosomal rna |
| url | https://agriculturalscience.unmerbaya.ac.id/index.php/agriscience/article/view/132 |
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