Replicon-Dependent Differentiation of Symbiosis-Related Genes in Sinorhizobium Strains Nodulating Glycine max

Guo, Hui; Wang, En Tao; Zhang, Xing Xing; Li, Qin Qin; Zhang, Yan Ming; Tian, Chang Fu; Chen, Wen Xin

doi:10.1128/aem.03037-13

Cited by 27 publications

(28 citation statements)

References 75 publications

(126 reference statements)

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“…The transfer of island genes into certain chromosomal backgrounds has also been observed in Bradyrhizobium strains isolated from other legume genera (54). A similar situation has been found with symbiosis plasmids in Rhizobium and Sinorhizobium species (60)(61)(62). Genetic divergence and gene flow.…”

Section: Resultsmentioning

confidence: 64%

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

Zhang

Guo

Wang

et al. 2014

Appl Environ Microbiol

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The genus Bradyrhizobium has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among Bradyrhizobium strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (SMc00019, thrA, and truA). This was also supported by analyses of eight genes outside the symbiosis island ("off-island" genes; SMc00019, thrA, truA, fabB, glyA, phyR, exoN, and hsfA). However, seven genes inside the symbiosis island ("island" genes; nifA, nifH, nodC, nodV, fixA, trpD, and rhcC2) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored by Bradyrhizobium japonicum, Bradyrhizobium diazoefficiens, Bradyrhizobium huanghuaihaiense, Bradyrhizobium liaoningense, Bradyrhizobium daqingense, Bradyrhizobium sp. I, Bradyrhizobium sp. III, and Bradyrhizobium sp. IV) was not found in Bradyrhizobium yuanmingense, Bradyrhizobium sp. II, or Bradyrhizobium elkanii. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes. Soybeans (Glycine max L.) were first domesticated in China and then introduced into different parts of the planet (1), now with an annual harvest area of 100 million hectares around the world (FAO, 2011). Ninety percent of their production comes from the United States, Brazil, Argentina, China, and India (FAO, 2007(FAO, to 2011. One of the key features of soybean is its ability to form symbiotic nitrogen-fixing nodules with diverse rhizobial species (2, 3), implying its important role in sustainable agriculture. It has been recurrently reported that Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium liaoningense, Bradyrhizobium yuanmingense, and Sinorhizobium fredii could nodulate soybeans (2-5). Recently, Bradyrhizobium huanghuaihaiense, Bradyrhizobium daqingense, Sinorhizobium sojae, and several unnamed species were also found to be effective microsymbionts of soybeans (2, 3, 6-8). Strain USDA110 represents a widely distributed type formerly known as B. japonicum Ia, but it has recently been proposed as a member of the new species Bradyrhizobium diazoefficiens (9).Recent studies not only suggested differences in the biogeographic distribution of rhizobial species nodulating soybeans but also demonstrated a biased selection of rhizobial species by different genotypes of soybeans (2,4,10,11). Consistent with these findings, comparative genomics of rhizobia revealed that the phyletic distribution of rhizobial functional genes involved in environmental adaptations and symbiotic interactions generally agrees with the phylogeny of rhizobial species (7). Therefore, it is important to distinguish different rhizobial species and even subdivis...

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Section: Resultsmentioning

confidence: 64%

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

Zhang

Guo

Wang

et al. 2014

Appl Environ Microbiol

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“…The genes nodM and nodT, coding the glucosamine-fructose-6-phosphate aminotransferase and an outer membrane lipoprotein of the RND efflux system, respectively, are known as symbiosis-related genes, which may play a role in the biosynthesis and secretion of Nod factors (Guo et al 2014;Lohrke et al 1998;Pinto et al 2009;Rivilla et al 1995). Only these two genes were studied in the work presented, although some other genes, which can be essential for the development of successful symbiotic interactions, were also discovered: the genes coding beta (1-6) glucans synthase (Bhagwat et al 1999), glycosyl Fig.…”

Section: Amplification and Phylogenetic Analysis Of The Nodm And Nodtmentioning

confidence: 99%

Extra-slow-growing Tardiphaga strains isolated from nodules of Vavilovia formosa (Stev.) Fed.

et al. 2015

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Eleven extra-slow-growing strains were isolated from nodules of the relict legume Vavilovia formosa growing in North Ossetia (Caucasus) and Armenia. All isolates formed a single rrs cluster together with the type strain Tardiphaga robiniae LMG 26467(T), while the sequencing of the 16S-23S rDNA intergenic region (ITS) and housekeeping genes glnII, atpD, dnaK, gyrB, recA and rpoB divided them into three groups. North Ossetian isolates (in contrast to the Armenian ones) were clustered separately from the type strain LMG 26467(T). However, all isolates were classified as T. robiniae because the DNA-DNA relatedness between them and the type strain LMG 26467(T) was 69.6% minimum. Two symbiosis-related genes (nodM and nodT) were amplified in all isolated Tardiphaga strains. It was shown that the nodM gene phylogeny is similar to that of ITS and housekeeping genes. The presence of the other symbiosis-related genes in described Tardiphaga strains, which is recently described genus of rhizobia, as well as their ability to form nodules on any plants are under investigation.

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“…Currently, rhizobia are grouped into symbiovars based mainly on nodC gene phylogenetic analyses and on symbiotic characteristics . The rchRST genes encoding conserved components of the type III secretion system (T3SS) have also been used in phylogenetic analyses of rhizobia as well as other core type III secretion genes, like rhcC2 and rhcJ . The rhizobial T3SSs contribute in nodulation in a manner depending on the host legume though they are not present in all rhizobia .…”

Section: Introductionmentioning

confidence: 99%

A novel symbiovar (aegeanense) of the genus Ensifer nodulates Vigna unguiculata

et al. 2017

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Replicon-Dependent Differentiation of Symbiosis-Related Genes in Sinorhizobium Strains Nodulating Glycine max

Cited by 27 publications

References 75 publications

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

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

Extra-slow-growing Tardiphaga strains isolated from nodules of Vavilovia formosa (Stev.) Fed.

A novel symbiovar (aegeanense) of the genus Ensifer nodulates Vigna unguiculata

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