A PCR primer design method for identifying spider mite species using k-mer counting.
Using PCR to distinguish closely related species can be difficult because they may have very similar genomes. Advances in bioinformatics make it possible to design PCR primers that are species-specific. In this study, we developed a bioinformatics method for extracting species-specific primer candid...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2025-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0321199 |
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| author | Tomoko Matsuda Hironori Sakamoto Takumi Kayukawa Yasuki Kitashima Toshinori Kozaki Tetsuo Gotoh |
| author_facet | Tomoko Matsuda Hironori Sakamoto Takumi Kayukawa Yasuki Kitashima Toshinori Kozaki Tetsuo Gotoh |
| author_sort | Tomoko Matsuda |
| collection | DOAJ |
| description | Using PCR to distinguish closely related species can be difficult because they may have very similar genomes. Advances in bioinformatics make it possible to design PCR primers that are species-specific. In this study, we developed a bioinformatics method for extracting species-specific primer candidate sequences (i.e., unpaired primers that were specific to a single species) from RNA-Seq data sets of 19 species of spider mites (Acari, Tetranychidae). Using k-mer counting, we obtained between 257 and 48,621 species-specific unpaired primer candidates for the 19 species. We then manually obtained a second primer that was also species-specific. The primer pairs were then confirmed to work in the target species and not to work in the non-target species. Finally, species-specific primer pairs were obtained for 17 of the 19 species tested. Such species-specific primers may be used for practical species discrimination by optimizing multiplex PCR. Our primer design method is expected to be applicable to other taxa. |
| format | Article |
| id | doaj-art-df7db8f5a1864cf1bf700140a3f52830 |
| institution | OA Journals |
| issn | 1932-6203 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-df7db8f5a1864cf1bf700140a3f528302025-08-20T02:31:44ZengPublic Library of Science (PLoS)PLoS ONE1932-62032025-01-01206e032119910.1371/journal.pone.0321199A PCR primer design method for identifying spider mite species using k-mer counting.Tomoko MatsudaHironori SakamotoTakumi KayukawaYasuki KitashimaToshinori KozakiTetsuo GotohUsing PCR to distinguish closely related species can be difficult because they may have very similar genomes. Advances in bioinformatics make it possible to design PCR primers that are species-specific. In this study, we developed a bioinformatics method for extracting species-specific primer candidate sequences (i.e., unpaired primers that were specific to a single species) from RNA-Seq data sets of 19 species of spider mites (Acari, Tetranychidae). Using k-mer counting, we obtained between 257 and 48,621 species-specific unpaired primer candidates for the 19 species. We then manually obtained a second primer that was also species-specific. The primer pairs were then confirmed to work in the target species and not to work in the non-target species. Finally, species-specific primer pairs were obtained for 17 of the 19 species tested. Such species-specific primers may be used for practical species discrimination by optimizing multiplex PCR. Our primer design method is expected to be applicable to other taxa.https://doi.org/10.1371/journal.pone.0321199 |
| spellingShingle | Tomoko Matsuda Hironori Sakamoto Takumi Kayukawa Yasuki Kitashima Toshinori Kozaki Tetsuo Gotoh A PCR primer design method for identifying spider mite species using k-mer counting. PLoS ONE |
| title | A PCR primer design method for identifying spider mite species using k-mer counting. |
| title_full | A PCR primer design method for identifying spider mite species using k-mer counting. |
| title_fullStr | A PCR primer design method for identifying spider mite species using k-mer counting. |
| title_full_unstemmed | A PCR primer design method for identifying spider mite species using k-mer counting. |
| title_short | A PCR primer design method for identifying spider mite species using k-mer counting. |
| title_sort | pcr primer design method for identifying spider mite species using k mer counting |
| url | https://doi.org/10.1371/journal.pone.0321199 |
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