Cookbook for plant genome sequences

Abstract Access to genome sequences is crucial to investigate and engineer traits in plants, explore biodiversity, and support phylogenetic studies. Over the last decade, affordable sequencing devices have substantially increased the size of the genomics community by enabling individual research groups to sequence the genomes of plant species of interest. There has also been a quick development of novel tools for sequencing data analysis. Here, we share experiences with plant long-read genomics methods for Oxford Nanopore Technologies (ONT) and provide hands-on guidelines to support newcomers entering plant genomics. The full workflow from planning a plant genome sequencing project to the public release of associated data sets is covered.