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.