Integration Of Rhizobia Omics Data And Construction Of A Database

The nitrogen fixation from the symbiosis between rhizobia and legume plants accounts for approximately one-quarter of the global annual nitrogen fixation on earth,which is of great significance for achieving sustainable agriculture.Researchers have conducted extensive studies on the distribution of rhizobia in bacteria taxas,the evolutionary history of the symbiotic ability,and the molecular mechanism of symbiotic nitrogen fixation in the rhizobia-legume plant system for decades.However,despite the significant efforts made by researchers to discover the diversity of rhizobia,understand the molecular mechanisms of symbiotic nitrogen fixation,and infer the evolutionary history of rhizobia,these analyses have largely been limited to specific rhizobia branches and model strains,and research data and information have been scattered throughout the literature and underutilized due to poor management.This limits the large-scale systematic study of the mechanisms and evolutionary history of rhizobia symbiotic nitrogen fixation.Therefore,this dissertation developed RhizobiaWiki,a comprehensive and user-friendly platform for rhizobia research.It mainly includes important information on rhizobia and their close relatives,such as genomes,transcriptomes,pan-genomes,symbiotic gene clusters,horizontal gene transfer,and host information.The RhizobiaWiki database covers a large amount of rhizobia-related data currently available,including 6,380 rhizobia genomes,120 transcriptomes,4,181,400 genes,and 684 representative strains’ 16 S r RNA gene sequences.Based on these datasets,this dissertation further analyzed 1,999 plasmid replication and transfer capabilities,detected 320,650 potential horizontal transfer genes,constructed 2,190 symbiotic gene clusters,and established 1,330 pan-genomes,providing sufficient data support for large-scale and specific rhizobia collections’ evolutionary biology and comparative genomics research.RhizobiaWiki also provides research tools such as BLAST and rhizobia species classification tools,providing information support for the classification of rhizobia strains and molecular biology research.In addition,this dissertation utilized the average nucleotide identity(ANI)value with a threshold of 95% to analyze and revise the taxonomic status of bacterial strains in RhizobiaWiki.As a result,888 instances of incorrect species assignment were detected,and 2475 unassigned strains were added to their respective species.Statistical analysis showed that the distribution of known rhizobial genomic information is highly biased,with certain species(ANI groups)having higher levels of assembled genome data and more comprehensive genome data,while other species(ANI groups)lack sufficient high-quality assembled genome data.This information disparity is also found in rhizobia associated with different hosts and habitats.Therefore,obtaining genomic data for specific strains is crucial for more accurately describing the evolutionary history of rhizobia.Directly using existing inadequate datasets may lead to incomplete or even erroneous inferences of evolutionary history.In summary,the construction of RhizobiaWiki not only provides a feasible solution to the growing contradiction between the increasing omics data and the lack of a comprehensive platform for storage and annotation in the rhizobial field but also facilitates the integration of different omics data to understand the complex and multi-level symbiotic patterns of rhizobia.