Comprehensive genomic analysis of Sinorhizobium meliloti isolates associated with fenugreek (Trigonella foenum-graecum Linn.) from diverse agroclimatic regions of India

Sinorhizobium sp. enhances plant vitality and stress resilience and improves soil structure. Underscoring their significance as agriculturally important bioagents for increased agricultural productivity requires understanding their taxonomic and functional relationships and the genetic foundations and pathways that drive plant growth-promoting traits. Genome sequencing, comparative genomics, functional annotation, and hybrid genome assemblies can achieve these. Comparative genomic analyses revealed a close relationship between the studied strains and Sinorhizobium meliloti and Sinorhizobium kummerowiae, which was further supported by phylogenomic, ANI, AAI, and dDDH analyses. Gene family cluster analysis identified 5999 gene families in the FRNB45 strain, 6116 in the FRNB101 strain, and 5996 in the FRNB126 strain. Functional genomic analysis identified several biosynthetic gene clusters (BGCs) related to secondary metabolite production, including polyketides, non-ribosomal peptides (NRPs), and siderophores, highlighting the metabolic versatility of these strains. KEGG pathway analysis confirmed the presence of nitrogen fixation and phosphate solubilization pathways, genes associated with the synthesis of indole-3-acetic acid (IAA), and siderophores. These findings support the potential application of FRNB45, FRNB101, and FRNB126 as plant growth-promoting rhizobacteria (PGPR), particularly suited for diverse climatic conditions and high-altitude ecosystems. However, further experimental validation is required to confirm their efficacy and consistency under field conditions.