A cry for kelp Evidence for polyphenolic inhibition of Oxford Nanopore sequencing of brown algae

A cry for kelp : Evidence for polyphenolic inhibition of Oxford Nanopore sequencing of brown algae

© 2024 The Author(s). Journal of Phycology published by Wiley Periodicals LLC on behalf of Phycological Society of America.

Bibliographische Detailangaben
Veröffentlicht in:Journal of phycology. - 1966. - 60(2024), 6 vom: 20. Dez., Seite 1601-1610
1. Verfasser: Pearman, William S (VerfasserIn)
Weitere Verfasser: Arranz, Vanessa, Carvajal, Jose I, Whibley, Annabel, Liau, Yusmiati, Johnson, Katherine, Gray, Rachel, Treece, Jackson M, Gemmell, Neil J, Liggins, Libby, Fraser, Ceridwen I, Jensen, Evelyn L, Green, Nicholas J
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2024
Zugriff auf das übergeordnete Werk:Journal of phycology
Schlagworte:Journal Article DNA extraction genome macroalgae nanopore polyphenols sequencing Polyphenols DNA, Algal
Beschreibung
Zusammenfassung:© 2024 The Author(s). Journal of Phycology published by Wiley Periodicals LLC on behalf of Phycological Society of America.
Genomic resources have yielded unprecedented insights into ecological and evolutionary processes, not to mention their importance in economic and conservation management of specific organisms. However, the field of macroalgal genomics is hampered by difficulties in the isolation of suitable DNA. Even when DNA that appears high quality by standard metrics has been isolated, such samples may not perform well during the sequencing process. We here have compared Oxford Nanopore long-read sequencing results for three species of macroalgae to those of nonmacroalgal species and determined that when using macroalgal samples, sequencing activity declined rapidly, resulting in reduced sequencing yield. Chemical analysis of macroalgal DNA that would be considered suitable for sequencing revealed that DNA derived from dried macroalgae was enriched for polyphenol-DNA adducts (DNA with large polyphenols chemically attached to it), which may have led to sequencing inhibition. Of note, we observed the strongest evidence of sequencing inhibition and reduced sequence output when using samples dried using silica gel-suggesting that such storage approaches may not be appropriate for samples destined for Oxford Nanopore sequencing. Our findings have wide-ranging implications for the generation of genomic resources from macroalgae and suggest a need to develop new storage methods that are more amenable to Oxford Nanopore sequencing or to use fresh flash-frozen tissue wherever possible for genome sequencing
Beschreibung:Date Completed 26.12.2024
Date Revised 04.01.2025
published: Print-Electronic
Citation Status MEDLINE
ISSN:1529-8817
DOI:10.1111/jpy.13513