Europe’s knowledge
platform for legumes

Fabada is a traditional market class of common bean (Phaseolus vulgaris L.) cultivated in northern Spain, recognized for its distinctive seed phenotype with very large, white, and oblong seeds. High-throughput genotyping of this market class revealed that its genome is predominantly of Andean origin, with approximately 30 % introgression from the Mesoamerican gene pool. The de novo genome assembly of the A25 bean genotype, derived from the local cultivar ‘Andecha’ which belongs to the Fabada market class, is described. Two complementary technologies were used: PacBio (Sequel II) for long reads and Illumina (NovaSeq PE150) for short reads. The depth of coverage achieved was 112x for Illumina and 47x for PacBio. Genome assembly resulted in 468,9 Mbp (98.5 % BUSCO completeness), organized into 1363 scaffolds plus the mitochondrial and chloroplast genomes. Based on the reference genome (NCBI accession number GCF000499845.2), these scaffolds were organized into 11 chromosomes and 169 unplaced scaffolds. The mitochondrial genome was assembled based on that of P. vulgaris (NCBI accession number NC_045135). Two mitochondrial scaffolds were obtained, one of 371,437 bp, and the other of 11,183 bp. The chloroplast genome was assembled based on that of P. vulgaris (NCBI accession NC_009259.1), resulting in 161,310 bp. To the best of our knowledge, this is the first available genome of a common bean accession exhibiting recombination between the two major gene pools, Andean and Mesoamerican, and the second assembled genome of a European common bean.

In the context of a rapidly growing global population and significant climatic and environmental change, there is an urgent need to produce nutritious food in a sustainable manner. Some crops are underutilised in Europe, despite their suitability to local environments, viability for sustainable production and potential to improve diets. Rye (Secale cereale) has a long history of cultivation in Europe, yet is underutilised owing to complex historical, socio-cultural, socio-political, socio-economic and agronomic factors. This paper explores an innovative, cross-sectoral approach that harmonises existing datasets from archaeology, plant science, nutrition and policy, and establishes an interdisciplinary dialogue to tackle this challenge