Abstract
Main conclusion
An interesting AMF colonization microcosm has been detected in the roots of Pancratium maritimum (sea daffodil). Both sequencing techniques (Sanger and NGS) have been used for AMF characterisation, showing a balanced trade-off between pros and cons.
By Sanger and next generation sequencing of rRNA nuclear molecular markers (SSU–ITS–LSU and ITS2, respectively), the presence of AMF communities in the roots of P. maritimum was evaluated. Our results shed light on the presence of AMF in sea daffodil and the diversity of assemblages of AMF detected after Sanger sequencing of the SSU–ITS–LSU marker is much higher than that determined following NGS sequencing of ITS2 alone.
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Abbreviations
- AMF:
-
Arbuscular mycorrhizal fungi
- ITS:
-
Internal transcribed spacer
- LSU:
-
Large subunit
- NGS:
-
Next generation sequencing
- OTU:
-
Operational taxonomic unit
- SSU:
-
Small subunit
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Acknowledgements
We gratefully acknowledge the Nando and Elsa Peretti Foundation for funding the study (Project 2012-83). For field sampling of Pancratium maritimum, we would like to thank Prof. Paolo Colombo, Dr. Rosaria Perrone formerly from Dept. of Earth and Marine Sciences (University of Palermo, Italy), and Dr. Rossella Muoio and Giancarlo Sibilio from the Botanical Garden of Naples (University of Naples Federico II, Italy). Finally, a special thanks to the friend and colleague Prof. Domenico Fulgione (Dept. Biology, University of Naples Federico II) for his illuminating contribution on the NGS method.
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Alignments of SSU–ITS–LSU rDNA sequences (FASTA file) (fas 109 kb)
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De Castro, O., Avino, M., Di Maio, A. et al. Sanger and next generation sequencing in the characterisation of arbuscular mycorrhizal fungi (AMF) in Pancratium maritimum L. (Amaryllidaceae), a representative plant species of Mediterranean sand dunes. Planta 248, 1443–1453 (2018). https://doi.org/10.1007/s00425-018-2981-z
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DOI: https://doi.org/10.1007/s00425-018-2981-z