Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings

Abstract

<i>Mesorhizobium</i> is a genus of soil bacteria, some isolates of which form an endosymbiotic relationship with diverse legumes of the Loteae tribe. The symbiotic genes of these mesorhizobia are generally carried on integrative and conjugative elements termed symbiosis islands (ICESyms). <i>Mesorhizobium</i> strains that nodulate <i>Lotus</i> spp. have been divided into host-range groupings. Group I (GI) strains nodulate <i>L. corniculatus</i> and <i>L. japonicus</i> ecotype Gifu, while group II (GII) strains have a broader host range, which includes <i>L. pedunculatus</i>. To identify the basis of this extended host range, and better understand <i>Mesorhizobium</i> and ICESym genomics, the genomes of eight <i>Mesorhizobium</i> strains were completed using hybrid long- and short-read assembly. Bioinformatic comparison with previously sequenced mesorhizobia genomes indicated host range was not predicted by <i>Mesorhizobium</i> genospecies but rather by the evolutionary relationship between ICESym symbiotic regions. Three radiating lineages of Loteae ICESyms were identified on this basis, which correlate with <i>Lotus</i> spp. host-range grouping and have lineage-specific <i>nod</i> gene complements. Pangenomic analysis of the completed GI and GII ICESyms identified 155 core genes (on average 30.1 % of a given ICESym). Individual GI or GII ICESyms carried diverse accessory genes with an average of 34.6 % of genes unique to a given ICESym. Identification and comparative analysis of NodD symbiotic regulatory motifs - <i>nod</i> boxes - identified 21 branches across the NodD regulons. Four of these branches were associated with seven genes unique to the five GII ICESyms. The <i>nod</i> boxes preceding the host-range gene <i>nodZ</i> in GI and GII ICESyms were disparate, suggesting regulation of <i>nodZ</i> may differ between GI and GII ICESyms. The broad host-range determinant(s) of GII ICESyms that confer nodulation of <i>L. pedunculatus</i> are likely present amongst the 53 GII-unique genes identified.