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Planta

, Volume 248, Issue 6, pp 1443–1453 | Cite as

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

  • Olga De CastroEmail author
  • Mariano Avino
  • Antonietta Di Maio
  • Bruno Menale
  • Marco Guida
Original Article

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.

Keywords

DNA barcoding Illumina MiSeq ITS2 SSU–ITS–LSU Psammophilic plant Root Sea daffodil 

Abbreviations

AMF

Arbuscular mycorrhizal fungi

ITS

Internal transcribed spacer

LSU

Large subunit

NGS

Next generation sequencing

OTU

Operational taxonomic unit

SSU

Small subunit

Notes

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.

Supplementary material

425_2018_2981_MOESM1_ESM.fas (108 kb)
Suppl. File S1 Alignments of SSU–ITS–LSU rDNA sequences (FASTA file) (fas 109 kb)
425_2018_2981_MOESM2_ESM.docx (63 kb)
Supplementary material 2 (docx 62 kb)
425_2018_2981_MOESM3_ESM.xlsx (24 kb)
Supplementary material 3 (xlsx 23 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of BiologyUniversity of Naples Federico IINaplesItaly
  2. 2.DNATech srl, Spin-off Company of the University of Naples Federico IINaplesItaly
  3. 3.Department of Pathology and Laboratory MedicineWestern UniversityLondonCanada
  4. 4.Department of BiologyUniversity of Naples Federico IINaplesItaly

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