TY - JOUR

T1 - Detection of nucleotide modifications in bacteria and bacteriophages

T2 - Strengths and limitations of current technologies and software

AU - Nielsen, Tue Kjærgaard

AU - Forero-Junco, Laura Milena

AU - Kot, Witold

AU - Moineau, Sylvain

AU - Hansen, Lars Hestbjerg

AU - Riber, Leise

N1 - © 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd. Special Issue: ECOLOGICAL AND EVOLUTIONARY INFERENCES FROM LONG‐READ SEQUENCING

PY - 2023

Y1 - 2023

N2 - RNA and DNA modifications occur in eukaryotes and prokaryotes, as well as in their viruses, and serve a wide range of functions, from gene regulation to nucleic acid protection. Although the first nucleotide modification was discovered almost 100 years ago, new and unusual modifications are still being described. Nucleotide modifications have also received more attention lately because of their increased significance, but also because new sequencing approaches have eased their detection. Chiefly, third generation sequencing platforms PacBio and Nanopore offer direct detection of modified bases by measuring deviations of the signals. These unusual modifications are especially prevalent in bacteriophage genomes, the viruses of bacteria, where they mostly appear to protect DNA against degradation from host nucleases. In this Opinion article, we highlight and discuss current approaches to detect nucleotide modifications, including hardwares and softwares, and look onward to future applications, especially for studying unusual, rare, or complex genome modifications in bacteriophages. The ability to distinguish between several types of nucleotide modifications may even shed new light on metagenomic studies.

AB - RNA and DNA modifications occur in eukaryotes and prokaryotes, as well as in their viruses, and serve a wide range of functions, from gene regulation to nucleic acid protection. Although the first nucleotide modification was discovered almost 100 years ago, new and unusual modifications are still being described. Nucleotide modifications have also received more attention lately because of their increased significance, but also because new sequencing approaches have eased their detection. Chiefly, third generation sequencing platforms PacBio and Nanopore offer direct detection of modified bases by measuring deviations of the signals. These unusual modifications are especially prevalent in bacteriophage genomes, the viruses of bacteria, where they mostly appear to protect DNA against degradation from host nucleases. In this Opinion article, we highlight and discuss current approaches to detect nucleotide modifications, including hardwares and softwares, and look onward to future applications, especially for studying unusual, rare, or complex genome modifications in bacteriophages. The ability to distinguish between several types of nucleotide modifications may even shed new light on metagenomic studies.

U2 - 10.1111/mec.16679

DO - 10.1111/mec.16679

M3 - Journal article

C2 - 36052951

VL - 32

SP - 1236

EP - 1247

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 6

ER -