Complete Genome of an Alkali-Resistant Rhizobium anhuiense Symbiont of Pea Reveals Species-Specific Plasmid Fusion and Genomic Plasticity

The rhizosphere microbiome is crucial for plant growth and stress resilience in sustainable horticulture. Here, we report the complete genome assembly and functional characterisation of Rhizobium anhuiense Xianghu001, a nitrogen-fixing symbiont isolated from pea (Pisum sativum) root nodules. A hybrid assembly strategy combining PacBio reads and Illumina reads yielded a 7.36 Mb high-quality assembly comprising one chromosome, one megaplasmid and four accessory plasmids, encoding 6899 protein-coding genes, of which 66.64% are located on the chromosome. Phylogenomics and synteny confirmed its placement within R. anhuiense. We detected a lineage-specific plasmid fusion forming the megaplasmid, while three accessory plasmids appear to be strain-specific and potentially acquired via horizontal gene transfer. Insertion sequence profiling suggests genome rearrangement shaping plasmid structure. To explore intraspecies diversity, we sequenced six additional local R. anhuiense isolates from pea. Despite their close geographic origin, genomic comparison revealed extensive divergence. Phenotypic assays demonstrated that Xianghu001 significantly promotes pea growth under nitrogen-deficient conditions, increasing chlorophyll content and nitrogen accumulation. It synthesises high levels of IAA (~184 mg/L), tolerates mild salinity (≤ 0.15% NaCl) and grows optimally at alkaline pH (8.0-10.0). Our findings provide a comprehensive genomic and functional framework for R. anhuiense Xianghu001 and underscore its potential as a biofertiliser.