Comparative Genomics Of Rhizobia Nodulate With Sesbania Cannabina(Retz.) Pers.

Sesbania cannabina(Retz.)Pers.is a pioneer green fertilizer crop for improving barren soil such as saline-alkali land.Based on our previous studies,the diversity of rhizobia nodulating with sesbania is relatively rich including 16 species of rhizobia belonging to 4 genera: Sinorhizobium,Rhizobium,Agrobacterium,and Neorhizobium.However,its symbiotic genes are highly conserved and clustered into a single branch on the phylogenetic tree,indicating that sesbania has a strong selectivity for symbiotic genes,and its symbiotic genes exhibit a significant horizontal gene transfer phenomenon.While the transfer mode and number of symbiotic genes are not yet clear,and it needs to be revealed through genome-wide bioinformatics analysis.Based on this,this study conducted whole genome sequencing analysis on the rhizobia sesbania and assembled the complete map,then systematically analyzed the characteristics and transfer ability of symbiotic plasmids.This study measured and assembled complete genome map of rhizobia nodulating with sesbania distributed in 4 genera and 12 species.Statistical analysis showed that the number of replicon was 3～8,and the genome size was 6.0 Mb～8.1 Mb.Each strain has one symbiotic plasmid,whose size from 350 kb to 500 kb and GC content from 57.7% to59.5%,which is lower than that of chromosomes and other plasmids.COG annotation analysis using Egg NOG showed that the CDS function of symbiotic plasmids of all strains was identified as 19 categories with contains three main functional categories: DNA replication,recombination and repair(L);energy generation and conversion(C);amino acid transport and metabolism(E).KEGG analysis shows that the CDS of symbiotic plasmids is divided into 35 metabolic pathways,mainly including membrane transport,amino acid metabolism,carbohydrate metabolism,and exogenous biodegradation and metabolism.The core symbiotic genes of rhizobia nodulating with sesbania include nod ABCFSUZ and noe P which distribute in two clusters: nod ABCSUIJ and noe CHOP.The core genes for nitrogenase synthesis are nif BDEHKMN(a total of 7),which distribute in three clusters:nif ABZT～fdx N,nif HDKENX,and nif SW.The genes of the type III secretion system(T3SS),except for Agrobacterium pussense IRBG74 and Sinorhizobium sesbaniae YTUZZ001,the other 10 species of rhizobia nodulating with sesbania all contain the T3 SS core gene.Analysis of the conjugation transfer system shows that the symbiotic plasmid of S.alkalisoli YIC4027、S.psoraleae CCBAU 65632、S.kostiense YTU21654、R.binae YTUBH007、Rhizobium sp.YTUZZ027、Rhizobium sp.YTUHZ045、Rhizobium sp.YTUHZ044 can autonomously undergo conjugation transfer.The phylogenetic analysis of the symbiotic plasmids showed that the symbiotic plasmids of all rhizobia nodulating with sesbania had a common descent,and the strains of Sinorhizobium were scattered in the phylogenetic tree,indicating that it took a long time to obtain the symbiotic plasmids.The strains of Rhizobium obtained the symbiotic plasmids the latest,which originated from Sinorhizobium.While Neorhizobium originated it earlier and lost the ability to transfer and evolved independently in evolution.In summary,this study explored the mechanism and transfer strategy of high-frequency transfer of symbiotic nitrogen fixing genes in rhizobia through comparative genomics methods,providing a theoretical basis for the adaptive evolution of rhizobia.