Results
We previously characterised 196 Rlt genomes isolated from pink nodules collected from 40 plots in three clover breeding trial sites at Rennes in France (F), Didbrook in England (UK), and Store Heddinge in Denmark (DK), as well as from 50 fields on Danish organic farms (DKO) (Figure 1 ). The strains were distributed throughout five of the seven known genospecies for Rl , with some genospecies being highly site-specific. gsC was the dominant genospecies at all sites except the UK trial site, where only gsB was present. Conversely, gsB was only found at the UK site.
To investigate whether this set of 196 genomes is representative of theRlt diversity at the sampled sites we collected nodules from the plots within the trials sites and the organic fields, leaving us with a total of 170 samples of nitrogen-fixing white clover root nodules from European field sites (Figure 1, Figure S1 ). Using the MAUI-seq method , 100 pooled nodules per sample yielded genotype frequencies of two core (rpoB and recA ) and two accessory (nodAand nodD ) genes in 170 samples. After filtering for samples with missing data or low UMI count, 105 rpoB samples, 153 recAsamples, 129 nodA samples, and 130 nodD samples were used for downstream analysis.