Long-read sequencing for epigenomic studies in the fields of ecology and evolution

Epigenetic mechanisms, including DNA methylation, play crucial roles in regulating gene expression, influencing phenotypic variation and facilitating responses to environmental pressures. Bisulfite sequencing has long been the gold standard for studying DNA methylation in ecological and evolutionary contexts. However, this method has significant limitations, including the difficulty in distinguishing C/T single nucleotide polymorphisms from methylation calls, susceptibility to bias from structural variants and an inability to detect specific modifications like 5-hydroxymethylcytosine. While some limitations of bisulfite sequencing can be addressed through careful study design or analytical strategies, the advent of long-read sequencing offers a powerful alternative by directly sequencing native DNA to overcome these limitations. Long-read sequencing provides comparable genomes and methylomes and enables the accurate detection of DNA methylation, facilitates haplotype phasing for allele-specific studies and resolves complex structural variation. Although challenges such as computational demands and elevated costs remain, rapid advancements in sequencing technologies, algorithmic efficiency and declining costs are improving accessibility. This perspective highlights the transformative potential of long-read sequencing on the study of epigenetics and genome evolution, offering a powerful tool to address critical questions in ecology and evolution. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.