Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T

Abstract

The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

Genetic Divergence of Bradyrhizobium Strains Nodulating Soybeans as Revealed by Multilocus Sequence Analysis of Genes Inside and Outside the Symbiosis Island

“…In contrast to some strains such as BTAi1 and ORS278, which use a Nod- independent pathway to form a symbiosis with Aeschynomene species (53), most Bradyrhizobium strains use the Nod-dependent strategy and are characterized by the genomic feature that key symbiotic functions are encoded by genes localized in a symbiosis island region (26,27). However, our understanding of the diversity of genes in this island is limited to nifH, nifD, and several nod/nol/noe genes, such as nodA, nodC, nodY, nodK, nodZ, nolL, and noeI (14,(18)(19)(20)54).…”

“…In this study, we aimed at providing high-resolution delineations and evolutionary genetics analyses of Bradyrhizobium strains nodulating soybeans in China by studying seven genes (nifA, nifH, nodC, nodV, fixA, trpD, and rhcC2) on the symbiosis island ("island" genes) and eight "off-island" genes (SMc00019, thrA, truA, fabB, glyA, phyR, exoN, and hsfA) (17,(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32). Strains were assigned to genospecies based on the phylogeny and ANI values of core genes SMc00019, truA, and thrA.…”

Genome Analysis Suggests that the Soil Oligotrophic Bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) Is a Nitrogen-Fixing Symbiont of Aeschynomene indica

“…The establishment of symbiosis between legumes and nitrogen-fixing (brady)-rhizobial bacteria generally starts with the exchange of chemical signals, that is, flavonoids and Nod factors, between the partners (33). In this symbiotic system, the sets of bacterial gene clusters for symbiosis (e.g., nod and nif) are located on a symbiotic plasmid or in a horizontally acquired chromosomal region (symbiosis island) (11,12,31). Therefore, the transfer of symbiotic gene clusters is generally considered to turn nonrhizobia into rhizobia (i.e., nonrhizobial strains that acquire a symbiotic gene cluster become rhizobia) (10,13).…”

“…To form functional nodules, some rhizobia utilize a type III secretion system to transport bacterial effector proteins into the cytoplasm of target eukaryotic cells (38). In B. japonicum, the rhc genes that encode core components of a type III secretion systems are found on a symbiotic island (11,31). There were homologous genes in the S58 genome showing low (less than 60%) levels of amino acid identity (see Table S5 in the supplemental material); these genes were probably acquired by lateral gene transfer, because the GC content of this region of the S58 genome is lower (Fig.…”

“…T (11) and of Mesorhizobium loti MAFF303099 (12). Nonsymbiotic (brady)rhizobia lacking the symbiotic gene clusters are often found among these species, including Bradyrhizobium sp.…”