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

Abstract

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.

Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi

“…These comparisons show the clear advantage of the se quen cetargeted NGS approach as contrasted with the alternative cloning-sequencing method for AMF species identification. However, the main disadvantage of the Illumina MiSeq are relatively short reads (250 bp ×2), which do not allow the use of long markers, such as the entire cloned SSUITS15.8S ITS2LSU region that was most often used for AMF barcod ing from 2009 to 2012 (Krüger et al, 2009;De Castro et al, 2018). A prerequisite for the correct AMF identification by the MiSeq method is the employment of a short marker region for sequencing (400-500 bp).…”