High-quality chromosome-scale genome assemblies of 29 maize inbred lines of European breeding relevance

Although several maize genome assemblies are publicly available, those of lines important to European breeding programs are underrepresented. Using PacBio long-read sequencing, we assembled high-quality chromosome-level genomes of 29 key lines of European breeding relevance, encompassing Northern flint and European flint lines used for adaptation to Northern European climate, lines derived from European landraces of tropical origin, and American temperate dent lines adapted to European regions. Genome assembly sizes range from 2.17 to 2.35 gigabases, with scaffold N50s ranging from 219 to 254 megabases. Completeness assessment revealed BUSCO scores ranging from 97.7 to 98.5 and merqury completeness scores ranging from 96.62 to 98.30. Calling structural variants and SNPs relative to the B73 reference sequence revealed the expected separation of inbred groups. Flint lines contribute the highest number of novel variants, thus emphasizing the importance of sequencing flint material to complete the maize pangenome. These high-quality genome assemblies therefore provide new opportunities to understand the dynamics of maize structural variation, and to identify the functional variations underlying maize phenotypic diversity.