A primer on pollen assignment by nanopore-based DNA sequencing
The possibility to identify plants based on the taxonomic information coming from their pollen grains offers many applications within various biological disciplines. In the past and depending on the application or research in question, pollen origin was analyzed by microscopy, usually preceded by ch...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Ecology and Evolution |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fevo.2023.1112929/full |
| _version_ | 1797871027278053376 |
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| author | Lisa Prudnikow Birgit Pannicke Röbbe Wünschiers |
| author_facet | Lisa Prudnikow Birgit Pannicke Röbbe Wünschiers |
| author_sort | Lisa Prudnikow |
| collection | DOAJ |
| description | The possibility to identify plants based on the taxonomic information coming from their pollen grains offers many applications within various biological disciplines. In the past and depending on the application or research in question, pollen origin was analyzed by microscopy, usually preceded by chemical treatment methods. This procedure for identification of pollen grains is both time-consuming and requires expert knowledge of morphological features. Additionally, these microscopically recognizable features usually have a low resolution at species-level. Since a few decades, DNA has been used for the identification of pollen taxa, as sequencing technologies evolved both in their handling and affordability. We discuss advantages and challenges of pollen DNA analyses compared to traditional methods. With readers with little experience in this field in mind, we present a hands-on primer for genetic pollen analysis by nanopore sequencing. As our lab mainly works with pollen collected within agroecological research projects, we focus on pollen collected by pollinating insects. We briefly consider sample collection, storage and processing in the laboratory as well as bioinformatic aspects. Currently, pollen metabarcoding is mostly conducted with next-generation sequencing methods that generate short sequence reads (<1 kb). Increasingly, however, pollen DNA analysis is carried out using the long-read generating (several kb), low-budget and mobile MinION nanopore sequencing platform by Oxford Nanopore Technologies. Therefore, we are focusing on aspects for palynology with the MinION DNA sequencing device. |
| first_indexed | 2024-04-10T00:37:48Z |
| format | Article |
| id | doaj.art-c19b0685fe6e45aaab1966bc4f105c3a |
| institution | Directory Open Access Journal |
| issn | 2296-701X |
| language | English |
| last_indexed | 2024-04-10T00:37:48Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-c19b0685fe6e45aaab1966bc4f105c3a2023-03-14T12:38:27ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2023-03-011110.3389/fevo.2023.11129291112929A primer on pollen assignment by nanopore-based DNA sequencingLisa PrudnikowBirgit PannickeRöbbe WünschiersThe possibility to identify plants based on the taxonomic information coming from their pollen grains offers many applications within various biological disciplines. In the past and depending on the application or research in question, pollen origin was analyzed by microscopy, usually preceded by chemical treatment methods. This procedure for identification of pollen grains is both time-consuming and requires expert knowledge of morphological features. Additionally, these microscopically recognizable features usually have a low resolution at species-level. Since a few decades, DNA has been used for the identification of pollen taxa, as sequencing technologies evolved both in their handling and affordability. We discuss advantages and challenges of pollen DNA analyses compared to traditional methods. With readers with little experience in this field in mind, we present a hands-on primer for genetic pollen analysis by nanopore sequencing. As our lab mainly works with pollen collected within agroecological research projects, we focus on pollen collected by pollinating insects. We briefly consider sample collection, storage and processing in the laboratory as well as bioinformatic aspects. Currently, pollen metabarcoding is mostly conducted with next-generation sequencing methods that generate short sequence reads (<1 kb). Increasingly, however, pollen DNA analysis is carried out using the long-read generating (several kb), low-budget and mobile MinION nanopore sequencing platform by Oxford Nanopore Technologies. Therefore, we are focusing on aspects for palynology with the MinION DNA sequencing device.https://www.frontiersin.org/articles/10.3389/fevo.2023.1112929/fullpollenDNA metabarcodingnanopore sequencingbarcodepalynology |
| spellingShingle | Lisa Prudnikow Birgit Pannicke Röbbe Wünschiers A primer on pollen assignment by nanopore-based DNA sequencing Frontiers in Ecology and Evolution pollen DNA metabarcoding nanopore sequencing barcode palynology |
| title | A primer on pollen assignment by nanopore-based DNA sequencing |
| title_full | A primer on pollen assignment by nanopore-based DNA sequencing |
| title_fullStr | A primer on pollen assignment by nanopore-based DNA sequencing |
| title_full_unstemmed | A primer on pollen assignment by nanopore-based DNA sequencing |
| title_short | A primer on pollen assignment by nanopore-based DNA sequencing |
| title_sort | primer on pollen assignment by nanopore based dna sequencing |
| topic | pollen DNA metabarcoding nanopore sequencing barcode palynology |
| url | https://www.frontiersin.org/articles/10.3389/fevo.2023.1112929/full |
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