From plant genomes to phenotypes

•Plant genome sequencing is maturing overcoming issues due to the genomes' repetitiveness increasing bioinformatics needs.•Plant Phenotyping is creating new needs for data standardization, analysis and storage.•The de.NBI node GCBN contributes services, expertise and training towards plant genome and phenome analysis.

Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis.Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.