Does peptide-nucleic acid (PNA) clamping of host plant DNA benefit ITS1 amplicon-based characterization of the fungal endophyte community?

Anete Borodušķe (Corresponding Author), Juris Ķibilds, Dāvids Fridmanis, Dita Gudrā, Maija Ustinova, Māris Seņkovs, Vizma Nikolajeva

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

Fungal endophyte community amplicon sequencing can lose a significant number of informative reads due to host-plant co-amplification. Blocking of plant-specific sequences with peptide nucleic acid (PNA) clamps has been shown to improve metrics of detected microbial diversity in studies targeting 16S and 18S regions of rRNA genes. However, PNA clamping has not been applied to the plant ITS region of rRNA gene – a widely accepted fungal marker. By applying PNA clamping technique to ITS amplicon sequencing of the endophytic fungal community of elderberry this study shows that PNA clamping significantly reduces host-plant co-amplification with the universal ITS1/ITS4 primer set. However, PNA clamping in combination with the discriminatory ITS1F/ITS2 primer set did not improve the metrics of fungal endophyte community ITS amplicon Illumina sequencing. This study shows that PNA clamping does not add practical benefit to taxonomic profiling of plant-associated fungal communities if the primers are already specific enough to exclude amplification of host DNA.

Original languageEnglish
Article number101181
JournalFungal Ecology
Volume61
DOIs
Publication statusPublished - Feb 2023
Externally publishedYes

Keywords*

  • Amplicon sequencing
  • Co-amplification
  • Fungal endophyte
  • Host-plant
  • ITS
  • PNA clamp
  • Sambucus nigra

Field of Science*

  • 2.8 Environmental biotechnology
  • 2.7 Environmental engineering
  • 1.5 Earth and related Environmental sciences
  • 1.6 Biological sciences

Publication Type*

  • 1.1. Scientific article indexed in Web of Science and/or Scopus database

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